This paper aims to compare the similarities and difference between the flood myths in China and Japan, and to explore the inheritance and evolution of cultural idea in the two countries.Firstly, the myth of the Gonggong Zhuanxu flood, the myth of Fuxi Nuwa and the flood myth of ethnic minorities in Chinese mythology are the main axis. Then, the flood myth in the two ancient books of Japan mythology, KOJIKI and NIHONSHOKI, are used as a singular to compare the similarities and difference between Chinese mythology and Japan mythology. In the genesis of Japan, the gods of Japan are only the titles of the word“MIKOTO” that often appear, which is an important key to the discussion of Japanese culture, and the marriage of brother and sister in the flood myth of China and Japan is that the early myth of Japan may have been influenced by the migration of Chinese immigrants.