It would be impossible for me to pick out one single theme for the book, particularly because you never do find out exactly what Nemo's motivations are. Because his character drives so much of the story, it is hard to know what the theme is. Is he destroying all of these ships because of what happened to his family or does he act in some ways as a revolutionary character or someone acting to protect indigenous cultures?
One theme is certainly the amazing variety and wonderous nature of the world beneath the waves. Nemo and Aronnax share in their incredible love for the sea and a fascination with the creatures they observe, so much so that it is very difficult for Aronnax to leave when he is finally convinced that he ought to escape.