This film is significantly autobiographical, reflecting Miyazaki's personal childhood stories: evacuation, loss of the mother, father's employment by a fighter plane production firm. In some sense, he retells the story of his life and his works. This movie also contains a theme of generational connections, their complexity and importance, reflected through endless labyrinths, being some form of Miyazaki’s will that he wants to keep for the future generations.

Like many other Miyazaki works, for example, Howl's Moving Castle, The Boy and the Heron includes pacifist ideas. It reflects on the idea of a "world without conflicts" and the possibility of its existence. It is less optimistic than Howl’s Moving Castle that has a happy ending; in The Boy and Heron, the fantastic world faces the cruelty of the real world. The film translates the idea that sometimes we can not change our world and escape war, pain and death. However, it still gives hope and shows the importance of warm personal connections and good intentions that matter even more in this harsh world.

Both the ideas of generational connections and world peace are intertwined with a reflection about the role of art. The film translates the idea of the importance of artwork in difficult times, it shows how the ideal fantastic peaceful world can coexist in our mind with the real world that is full of unpleasant things. The whole second part of the film unfolds more in the characters' imagination rather than in real life, but this fantasy world helps Mahito to learn a lot about reality. Moreover, even though the created fantastic world is ruined in the end, as well as many of Miyazaki’s other worlds do, there is a hope that there will be someone who will find a new idea and create a new incredible world. The final frame with an empty room is a great metaphor for a place where something good has ended, but something even better can be created.

On the one hand, The Boy and the Heron follows the traditional pattern of a fairy tale: there is a main character, his guide and the tough way that they have to overcome, traveling between worlds. As for fantastic creatures, there are traditionally a lot of them. For example, we can see Wara Wara – interestingly reminding the creatures from Princess Mononoke, Kodama stones – flying white creatures representing the unborn souls. The Heron itself is a fantastic creature, too. It plays an important role as a guide. On the other hand, the structure is much more complex than this traditional plot fishbone, there are a lot of fantastic jumping changes of a frame.