Abstract: In order to understand the migratory ecological characteristics of Japanese eel (Anguilla japonica) in Pearl River water system and effectively protect the wild population of eel, a total of 155 Japanese eels were collected from 11 freshwater habitats such as Liuzhou, Heshan, Wuxuan, Guiping, Wuzhou, and one estuary habitat in Zhuhai. Using electron probe microanalysis to determine the ratio of Sr and Ca elements in otoliths and analyze the micro chemical Sr/Ca of otoliths, this study found that Japanese eel in the Pearl River has many migration patterns, such as “seawater-freshwater”, “seawater-estuarine-freshwater”, “seawater-estuarine-seawater-estuarine-freshwater”, and “seawater-estuarine-freshwater-estuarine-freshwater”. However, these eels ultimately towards freshwater habitats for the purpose of fattening. This observation underscores the adaptability of Japanese eel in the Pearl River to diverse habitats and salinity levels, exemplifying their flexible migration strategies across different water bodies. Furthermore, it accentuates the critical importance of safeguarding freshwater habitats.