John Wyndham wrote after World War II in which he served in the British Armed Forces and his stories reverberate with the theme of survival after world-wide holocaust. The Chrysalids fits into this thematic idea as an examination of survival decades after the event. In this book, Wyndham explores one of his greatest concerns, which is how human logic--usually a prized mental faculty--can turn to humanity's harm when events change the established order of life. This logic-turned-to-harm idea is perfectly illustrated in The Chrysalids because Wyndham shows quite clearly what happens when the old established order of existence is clung to in the face of great change: the purging of Blasphemies is what old logic brings about in Waknuk.
With this background in mind, the main theme of The Chrysalids centers around the need to reassess events and circumstances with new logic taking in new information that may never have existed before and incorporating it into a new order of thought. The major theme is that a future of hope awaits for those of humanity who will adapt their thinking to a changing world--this is true whether it changes by way of catastrophe or by way slowing churning time. Correlated themes are the inevitability of change, ignorance and bigotry.