Abstract: To investigate the environmental driving factors of habitat distribution for migratory, marine, and estuarine larval fishes in the Yangtze River estuary, based on the larval fish sampling data collected in the Yangtze River Estuary during September 2022 (Summer) and April 2023 (Spring), we applied the Maximum Entropy (MaxEnt) Model to analyze the habitat distribution characteristics and environmental driving mechanisms of Coilia mystus (Migratory species), Engraulis japonicus (Marine species) and Callionymus olidus (Estuarine species). The results reveal that the south branch exhibited higher sea surface temperature (SST), pH (SpH) and nutrient levels (SNITRO), while the north branch showed higher sea surface salinity (SSS) and chlorophyll concentration (SCHL). The MaxEnt model demonstrated strong predictive capability for habitat distribution of these three larval fishes AUC (Area under the curve) >0.8, with slightly better performance in spring than summer. Sea surface dissolved oxygen was the key factor influencing habitat distribution for both C. mystus (Relative contributions: 80.8% in spring and 86.6% in summer) and C. olidus (44.0% and 79.0%), whereas sea surface salinity dominated for E. japonicus (44.0% and 79.0%). There were significant differences in the habitat characteristics and key environmental factors of larval fish of different ecological types, leading to species-specific responses in their early life history replenishment processes to environmental changes. Therefore, the protection of juvenile fish resources in the Yangtze River Estuary requires development of differentiated protection strategies based on the biological characteristics and habitat needs of different ecological types of fish.