Love
The main theme of the movie is love. The movie begins with two people searching for each other, unaware that they are missing one another. Taki and Mitsuha find themselves in a strange situation where one wakes up in the body of the other. As time progresses, and they get to know each other through their lives and through messages they leave to each other, they begin to fall in love. One day, Mitsuha suddenly disappears from Taki's life, and he does everything he can to get her back before all the memories of her fade. Their love story is a fated one. They find each other at the end, despite having lost the memory of their encounter because the sensation of missing something from their lives remained.
The theme of the supernatural
The supernatural element is an important aspect of the movie. It is explored through tradition and religious beliefs. It turns out that Taki and Mitsuha found each other for a reason beyond themselves. They found each other to prevent a disaster, a comet that will fall on Itamari and take many lives, Mitsuha's included. They have to untwist the thread of time, meet at the twilight when there is a possibility to meet someone from another world. The supernatural element is the possibility of time travel and going back in time to change the devastating events, through the switching of consciousness from one body to another.
Time
The theme of time is explored in the movie in connection to religion regarding the idea of time. Time is compared to "musubi", to knotting of threads that twist and untangle and are connected again. Taki and Mitsuha untangle the knot of time, twist it to change the events that happened, following the comet-disaster on Itamari. They connect the thread of time to enable the flow of life again, and give each other the possibility to meet again in the future.