There is no one way to describe the atmosphere or mood of the story.
At the beginning of the novel, the mood is carefree and humorous. Tom is a mischievous boy who likes to have fun. He gets in trouble time and time again. The reader cannot but be amused at his behavior, such as when he says that David and Goliath are apostles, or when he falls in love with and engages Becky Thatcher, until Becky breaks up with him for his prior engagement with Amy Lawrence.
As the novel progresses, there are elements of suspense. When Huck and Tom witness the murder of Dr. Robinson by Injun Joe, there is a sense of fear and suspense. The reader wonders what will happen next, especially as there are several "close calls" for Tom and Huck with Injun Joe.
Finally, there is a mood of satisfaction as well, when justice finally comes to Injun Joe and when we see the maturation of Tom and the good fortune that befalls Huck. Things work out well in the end.