One theme of the story is the way the characters, particularly Mr. Shiftlet, miss God's grace by running away from it when it is right in front of them.

This is symbolized from the start when Mrs. Crater looks away from the sun (the light of God) and wants to shield herself from it. She runs away from God's light primarily by using material things. She wants to get rid of the presence of God in her life, which is her mute daughter Lucynell, who is described as an ‘‘angel of Gawd.’’

Mrs. Crater eventually "sells" this angel of God to Mr. Shiftlet, who gets no more satisfaction out of this than Judas did receiving money to betray Jesus. Mr. Shiftlet then abandons his chance for redemption when he leaves Lucynell in the diner and drives off.

At the end of the story, Mr. Shiftlet runs away from God's redemption once again. He feels the turnip-like clouds descending on him, and he prays to God to

"Break forth and wash the slime from this earth!"

God seems to answer his prayer with a cleansing rain, but instead of recognizing he is part of the slime that needs to be washed clean, Mr Shiftlet speeds in his car away from the purifying storm.

A theme of “The Life You Save Might Be Your Own” is focus on God versus material things.

At the beginning of the story, Mr. Shiftlet is a Jesus-like figure.  He is a tramp carpenter who passes by one day and talks philosophically with the “old woman” Mrs. Crater.  He is not interested in money or material possessions.

"Lady," he said in a firm nasal voice, "I'd give a fortune to live where I could see me a sun do that every evening."

Yet as he remains on her farm, Mrs. Carter corrupts him.  He first stays in an old car and does odd jobs for her for no money, but then he fixes the car.  He accepts money to marry her.  He becomes more interested in the material, and less interested in the spiritual.

The difference in Mr. Shiftlet’s character is especially evident when he picks up the hitchhiker.  He tells the boy how he has the best mother in the world, and it infuriates him such that he jumps out of the car.  As Mr. Shiftlet drives on, he realizes he has turned his back on God.  The sun he spoke of at the beginning of the story is covered with a cloud, and the rain hits his car.

What is the overall theme in the short story "The Life You Save May Be Your Own"?

One of the themes that plays a critical role in the story is the connected themes of religion and corruption.  There is religious symbolism in the story, Lucynell is referred to an an angel, Shiftlet cannot see this aspect about his wife, but all the other people in the diner can see that she is holy.

Mrs. Crater wants Shiftlet in her home so that he can fix broken things, she bargains with him and offers her daughter, indicating that people are less important than things.  The mother does not seem to find it wrong to offer her mute daughter to an odd stranger. 

The car seems to have more value in the story than Lucynell. And finally when Shiftlet leaves Lucynell at the diner, it is the final act of corruption.  He takes the car and leaves his wife who resembles an angel.  He abandons his salvation, Lucynell, only to grasp the material and continue wandering looking for meaning.

What is the overall theme in the short story "The Life You Save May Be Your Own"?

The main theme in this story is the quest for meaning. This need to find out what life means is common to O'Connor's works. In this story, it shows up in Shiftlet's wandering. In moving around, he isn't just traveling. He's looking for something, some meaning to it all. The meaning of life shows up in other symbolic ways as well—in what Lucynell is called (an angel), in the sign by the side of the road, and so on.

What is a universal theme for "The Life You Save May Be Your Own" by Flannery O'Connor?

Flannery O'Connor's stories often deal with God and religion, and these components are present in "The Life You Save May Be Your Own;" the universal theme I find in this short story deals with elements related to religion: salvation and redemption. The story of Mrs. Crater and Mr. Tom Shiftlet concentrate on:

an individual’s ability to find opportunities for salvation and redemption in everyday life.

It would seem that Lucynell, Mrs. Crater's daughter, is the only innocent in the story—the one truth her mother shares with Shiftlet. Lucynell is deaf, though quite able to help around the house and yard—a selling point Mrs. Crater shares with Tom. She is also described as "an angel of Gawd." And an angel she may well be, in that she has not been corrupted as has her mother is.

Mrs. Crater's name denotes an "emptiness," like a crater in the earth or on the moon. She is a manipulative woman who is willing to trade her daughter to get Mr. Shiftlet to stay. When she describes Lucynell on her wedding day, though it sounds as if she is complimenting her, Mrs. Crater is alluding to the fact that the girl is like a baby: Mrs. Crater shows how base she is in sacrificing this innocent to a man she hardly knows, simply to marry her daughter off and have a man on the premises to do the work she cannot do. She is not moving in the direction of redemption.

Don't Lucynell look pretty? Looks like a baby doll.

Tom Shiftlet is a man who is in need of salvation and redemption. He seems to be decent in the work he does when he agrees to stay: he helps fix a roof, the pig trough, etc. He teaches Lucynell her first word: bird. It is not until Mrs. Crater squeezes out what tenuous goodness there is within him with her devastating words that Tom Shiftlet (as his name seems to denote) "shifts"—he loses his faith and becomes something that even he is ashamed of. Mrs. Crater confronts him with harsh words to force the deal about the marriage:

...you'd be getting a permanent house...and the most innocent girl in the world. You don't need no money. Lemme tell you something: there ain't any place in the world for a poor disabled friendless drifting man.

These words pain him, and the simile referring to buzzards brings a vision of "death"— perhaps the death of his faith.

The ugly words settled in Mr. Shiftlet's head like a group of buzzards in the top of a tree.

Mr. Shiftlet is aware that a man is made of body and spirit. He knows that life is not only about money. His life a is struggle to find a place in the world because his is not "whole," physically or spiritually. Mrs. Crater's offer daughter and car, in exchange for his freedom, become a temptation, and when she sweetens the deal with money, he accepts. They travel into town and Shiftlet and Lucynell are married. The couple leaves, driving to Mobile—Shiftlet's destination.

They stop at a diner, and when Lucynell falls asleep at the counter, he abandons her there. As he continues on the trip, he is filled with a sense of shame. He realizes he has become as sinful as the world that surrounds him.

Although he could have found salvation in settling down on the Crater's farm, Tom allows Mrs. Crater's manipulation and her harsh words to define who he is. In continuing his trip to Mobile, we sense he has left behind his opportunity for salvation in turning his back on Lucynell and what he believes to be right.

Additional Source:

http://www.enotes.com/life-you-save-may-be-your-own/critical-overview