In aquatic ecosystems around the world, gobies comprise one of the most diverse groups of fishes in estuaries. The Yangtze River estuary, the biggest estuary in the western Pacific, is a major habitat for larval gobies, with the peak spawning and breeding season occurring during late spring and summer. To investigate the adaptation mechanism of larval gobies to environmental factors, three models (a global generalized linear model, a generalized additive model, and a geographically weighted Poisson regression) were used to simulate and forecast the major habitat distributions of larval gobies based on the survey data from 2018 to 2020. Six species of gobies were studied: Rhinogobius giurinu, Odontamblyopus rubicundus, Tridentiger barbatus, Parachaeturichthys polynema, Tridentiger trigonocephalus, and Trypauchen vagina. The habitats for brackish species T. barbatus were mainly in freshwater (where, using the practical salinity scale, salinity is 0-1) of the south branch, whereas the marine species P. polynema was mainly caught in oligohaline waters (where salinity is 1-5) of the north branch. The other euryhaline species were near the exit of the north branch or dispersed throughout the surveyed region. Year, season, salinity, and sample location had significant effects (P < 0.001) on determining the habitat distributions of larval gobies. The geographically weighted Poisson regression identified that the temperature, depth, distance from the coast, and chlorophyll a had a significant effect (P < 0.001) on the local distribution of habitats. This work supplements information about the distribution of major habitats and their interactions with the environment for the ecologically important species of goby in the Yangtze estuary during the larval stage, and the conclusions provide a basis for the management of aquatic ecosystems and biological habitats.