The title of this excellent story itself yield what is, to me, the central theme. By choosing a title including the word "Chrysalids," Wyndham points towards the way in which humanity is changing and developing, moving from its caterpillar state into something new. Of course, the fact that the title includes the words "chrysalids" indicates that this transformation and change is not completely over yet, and thus we are plunged into the frightening world of David and Rosalind and their companions, who recognise that they are different from the rest of the humans they live with, but must hide those differences.
The focus on transformation and evolution is likewise signalled by the woman from Sea Land, who states clearly that "life is change" and "The living form defies evolution at its peril; if it does not adapt, it will be broken." Thus the central theme of the novel points towards the way in which humanity is constantly changing and evolving and how we must embrace that.