As an important fishery resource in the Yangtze Estuary, has high nutritional value and delicious taste. Because of overfishing, environmental pollution, and habitat degradation in recent years, the resources of have declined sharply. As a type of migratory fish, the growth, development, and reproduction of are affected by the freshwater, estuarine brackish water, and seawater environment. Therefore, exploring the habitat history of is of great importance in the protection and management of this resource. To study the habitat history of in the Yangtze Estuary and its adjacent sea area, otolith microchemical analysis of 10 from Chongming Island in the Yangtze Estuary and its adjacent Lvsi sea area was conducted using X-ray electron probe microanalysis techniques. Quantitative line analysis and surface distribution of Sr content showed that Sr/Ca ratios in the otolith core area of existed in Sr/Ca<3, 3C. mystus could be divided into three types:the freshwater incubation field, estuarine brackish water incubation field, and sea water incubation field. The variation in Sr/Ca ratios in the individual otoliths from the core to the edge was highly significant, including low-ratio freshwater habitat (Sr/Ca<3, minimum 2.04±0.87) and high-ratio seawater habitat (Sr/Ca>7, maximum 7.81±0.91). Thus, the habitat history types of could be divided into four types:freshwater-estuarine brackish water type, estuarine brackish water settlement type, estuarine brackish water-seawater type, and freshwater-estuarine brackish water-seawater type. There were freshwater and estuarine brackish water hatching individuals whose habitat types included freshwater-estuarine brackish water type, estuarine brackish water-seawater type, and freshwater-estuary brackish water-seawater type in the adjacent sea area of the Yangtze Estuary. There were sea water and estuarine brackish water hatching individuals whose habitat types included freshwater-estuarine brackish water type, estuarine brackish water settlement type, and freshwater-estuary brackish water-seawater type in the Chongming Island sea area of the Yangtze Estuary. This reflected the similarities and differences between the individuals in Chongming Island and the Lvsi sea area in the Yangtze Estuary. Through this study, it is proved for the first time that there are three incubation sites and four habitat types in the Yangtze Estuary and its adjacent sea area, which accurately reflect the diversity and complexity of the individual composition and life history of .