You will have to decide what position you would like to take in your thesis, but here are a few ideas.

Flannery O'Connor's short story, "Good Country People," focuses on a mother/daughter relationship that is failing. Joy changes her name to Hulga, which irritates her mother in every possible way. Joy/Hulga also goes out of her way to act unpleasantly and says she believes in nothing. On the other hand, Mrs. Hopewell does not accept Joy/Hulga for who she is. She continues to call Joy/Hulga, Joy. As well, she disapproves of her daughter's education and even her daughter's dress.

Through this characterization, you could form a thesis such as:

Through the characterization of Mrs. Hopewell and her daughter, Joy/Hulga, in the short story, "Good Country People," Flannery O'Connor illustrates a failed mother/daughter relationship.

or

Flannery O'Connor weaves the theme of manipulation and its results through her characters' actions in the short story "Good Country People."
For this thesis, you could discuss how all the characters (or the characters you would like to discuss) try to manipulate each other and the effects of that manipulation.

Good Luck!

Your thesis statement is your position and lets your readers know what you intend to prove in your essay. The following are some ideas of possible positions you could take on Flannery O'Connor's short story, "Good Country People."

• Flannery O'Connor's use of situational irony in this story highlights the motivations of the characters. Joy, who renamed herself Hulga, is Mrs. Hopewell's thirty-two-year-old daughter with a false leg and a Ph.D. She meets a simple young man who is selling Bibles door-to-door, and is described by her mother as "salt of the earth." She believes he is innocent but is fooled when he uses her intellectual vanity to rob her. 
• Flannery O' Connor's story "Good Country People" is a study of the ways in which people deceive each other and themselves. Mrs. Hopewell deludes herself into thinking that if she has enough hope, things will turn out well for her daughter. She works at not seeing her daughter for who she is, but who she wants her to be. Joy/ Hulga uses her intellectual pride as a shield to keep others from knowing her in intimate ways. When she does concede to let someone in, Manley Pointer, she finds that he has deceived her completely. Manley Pointer is able to see Joy/ Hulga's weakness and exploit it for his own personal gain. He deceives others as a career and pastime. 
• No one is what they appear to be, especially not Good Country People. Mrs. Hopewell had a value of simple, honest, good people. She distinguishes this type of people from "trash." No one she knew, though—including herself—fit her description of Good Country People. Her daughter was sullen, dishonest, and prideful. Her help, Mrs. Freeman, was unable to admit wrongdoing in any way. Manley Pointer presented himself as good country folk, but he was a liar and con man. Mrs. Hopewell herself was self-deluded and shallow. She pretended to be kind and caring, but it was superficial at best.

What is a good thesis drawn from O'Connor's "Good Country People"?

This completely compelling story by O'Connor is filled with possible themes to explore in a literary analysis essay.  It is important to remember that a good essay is making an argumentative claim (thesis) and then writing an essay in which you prove that to be true with evidence from the text.  In order to focus your essay you need to think about which aspects of the story are most compelling to you and then go from there.  Are you drawn to a particular character?  Then ask yourself what that character's thoughts and actions contribute to the overall meaning of the novel.  Are you interested in a specific topic?  Then you need to ask yourself which events or characters help contribute to your understanding of that topic in the novel.

For example:  If you are interested in Mrs. Freeman as a character then ask yourself what does she add to the story?  Why does the story start and end with her?  How does she serve as a contrast to the other characters?  Your ANSWER to the question will be your thesis statement.  You could do this to create a thesis statement about any of the characters, but it makes sense to write about one of the four major characters.

If you are interested in themes and meaning then ask yourself "what truth of life did I learn by my reading this story?"  You certainly learn about the hypocrisy of human nature, and the difference between intelligence and common sense (book smarts vs. street smarts).  You learn about how people define themselves and how their world view shapes their interactions with others.  Choose one topic and then discuss how the characters and events of the story work to make that point.

If you need more topics, I would encourage you to look at the themes page here on enotes.