Japanese imperial narratives claim that Japan has the world’s oldest monarchy and as you say that the Naruhito can trace his lineage to Emperor Jimmu. Nevertheless, there are numerous issues with the historicity of such claims.

Early imperial narratives are mythological in nature. Jimmu for example is literally described as the grandson of a Goddess and is said to have lived to the age of 126. Indeed, scholars question the very existence of Japan’s first 9 emperors. Although there is some consensus that the 10th Emperor, Sujin, actually existed.

Modern scholars have also sought to argue that the writers of Japan’s imperial histories such as the Kojiki and Nihon Shoki, and interpreters of these texts have purposely attempted to overlook and redact information that suggests that the lineage of the imperial family is far from one unbroken line.

I’d recommend the work of Stefan Tanaka who explores how the myth of unbroken Japan’s imperial lineage has been used and developed following the Meiji Restoration.