Family and Legacy
The theme of family love is approached firstly by the book's central conflict—Jacob struggling to understand the death of his grandfather. The theme is then secondarily explored by the familial dynamic in Miss Peregrine's home and also by the fact that Jacob is in the same stage of life as his own grandfather when he was an orphan a long time ago.
The theme of family struggles to see legacy in a meaningful way, in that Jacob, instead of going forward, travels back in time and gets stuck in a time loop that ultimately ends in futility and obscurity when their ymbryne, Miss Peregrine, is lost as a bird forever. Something about the death of his grandfather makes Jacob's search for legacy and family frustrated and unattainable.
Death and Obscurity
Death is long known to frustrate man's sense of meaning. That theme is represented in the novel by the death of Jacob's grandfather, which initiates Jacob's (and the book's) central attempt to find meaning in the mysterious home. The idea of death—or cheating death—also appears in Enoch's skill with raising the dead as well as the wights and hollows' search for immortality.
This question is usually answered by a deus ex machina, or a surprisingly good ending to a difficult narrative. But, in Miss Peregrine's, the story resolves in a way that doesn't allow for easy closure. It leaves the question hanging. Is life meaningful in spite of death?
The Power of Youth
One of the most positive events of the novel occurs when Jacob and Emma defeat one of the hollows. This occurs because of a special ability of Jacob's, which allows him to see the monsters. The special abilities of peculiars, including Jacob, demonstrate that young people can accomplish great tasks. This does not solve all of their problems, however, and no one in the book can solve the problem surrounding the novel's final conflict. But again, this seems to be a human limitation, not a limitation specific to young people.
The Limitations of Knowledge
Jacob has an epiphany that he is also unique in that he can see the monsters that have been haunting him. This insight is symbolic and points out a limitation of knowledge, namely that we can only know what we can see. So, if there are things that go bump in the night, we wouldn't necessarily know about them if they weren't readily apparent. Jacob is special in the narrative because his unique insight helps him to see the monsters, and even to defeat one of them, although in the end he can't save the day.
Time
Time is a recurring theme throughout this novel, which tries to contradict our common perception of time as a linear, fixed entity. Instead, Miss Peregrine's paints time as fluid and manipulable. With time loops, many different times can exist at once, under the control of human hands. Granting humans—even peculiar humans—the ability to manipulate time gives them immense power, since we often view time as the one thing we cannot change.
Greed
This novel paints a clear picture of the dangers of greed and wanting what you cannot have. Miss Peregrine warns Jacob not to speak about the future to the peculiar children who are stuck in the time loop because she knows it would be detrimental for them to want something that is completely out of their reach.
The villains of the story—the wights and hollows—also want something they are not meant to have: immortality. Their desire for this unattainable goal causes much danger and places many lives in jeopardy, a clear caution against the kind of all-consuming greed that can drive a person to wreak such havoc.
Past vs. Present
Throughout the novel, the past often comes in conflict with the present, as Jacob attempts to sort out his life being lived with one foot in the loop and one foot outside of it. The most notable instance of this tension is his relationship with Emma. Her past relationship with his grandfather keeps encroaching on their feelings for each other now, and it is difficult for Jacob to separate this vision of Emma in the past with the girl he sees in front of him right now.
