The mood in the beginning of The Chrysalids is a sense of discovery. David is learning many new things about the society he lives in. Such examples of this are what people will do to save themselves (Aunt Harriet willing to switch babies and when that failed, to kill herself to save her baby and herself from a life of misery; and Sophie willing to experience incredible pain so that David would not find out about her mutated feet) and the landscape and traditions of the rest of the world. Uncle Axel teaches him about the lands around Waknuk and Labrador which are mostly deadly radioactive infernal regions. David also starts to learn about how people are different than those in Waknuk and what the definition of "normal" is. A feeling of discovery is thus an important part in this novel section.
The mood in the middle of this novel is a feeling of panic. Panic is an overwhelming emotion in this segment because this is when the shape-thinkers are discovered and David, Rosalind, and Petra must run for their lives. As everything that has ever been there for them is suddenly gone, these three must learn to fend for themselves in an unknown landscape. Sally and Katherine also feel the highest level of panic when they are captured and tortured. Rachel must live alone in a community that is suddenly acutely intent on finding deviations and Michael must act the part of a spy in order to save himself and the rest of the group. All these factors combine together to create a mood of panic and terror.
The mood in the end of the book is a feeling of relief and wonder. The characters feel relieved because they have been saved from a life of misery and wonder because they are taken to Sealand where a metropolitan city is waiting for them, home to thousands of shape-thinkers. Relief is a very important mood for this part of the novel because the main characters have been living a lie where they had to pretend to be something they are not. Now they can be free of any obligations and controlling laws.
Two themes that are prevalent in this novel are the idea of alienation of individuals in a society and the idea of creating a "perfect society". Through various examples in the novel such as not allowing Mutants to live in a society of people without deformities The Chrysalids proves that when you alienate people from a culture, the entire society suffers. The idea of creating a perfect society is one of the biggest themes in this novel. The entire society based in Waknuk is obsessed with the idea of being just like the Old People. Their false ideals lead to the destruction of their own community in the battle between the Fringe people and the Waknuk people. Readers can learn about the importance of believing in your own ideas and not letting a controlling society decide your fate.