As a typical tropical estuarine ecosystem, the Wanquan River estuary provides critical spawning and nursery habitats for various fish species. Its complex habitat conditions and hydrological dynamics significantly influence the distribution patterns of early fish resources. The Javanese goby (Pseudogobius javanicus) is the dominant species in the larval fish community of this region, highly sensitive to environmental changes, and serves as an important indicator species for assessing habitat quality. To identify the key driving factors and response relationships of its larval dynamics, this study conducted year-round monitoring from May 2021 to April 2022 at seven sites representing four habitat types within the Wanquan River estuary. Larval samples of P. javanicus and nine environmental variables were collected, and a two-stage generalized additive model (two-stage GAM) was constructed to evaluate larval responses to environmental factors. Results showed that the abundance of P. javanicus larvae exhibited marked seasonal and spatial heterogeneity, with significantly higher abundance during the rainy season (June to August) compared to the dry season. Mangrove edges and submerged vegetation areas had the highest larval abundance and were identified as core nursery habitats. The first-stage GAM (GAM1) revealed that temperature, ammonia nitrogen, dissolved oxygen, and chlorophyll-a were key factors influencing occurrence probability (cumulative deviance explained 77.6%, P < 0.05). The second-stage GAM (GAM2) indicated that salinity, pH, temperature, and chlorophyll-a jointly regulated larval abundance (cumulative deviance explained 77.3%, P < 0.05). The two-stage GAM identified optimal "environmental windows" as temperature 26–30 ℃, salinity 10–15 ppt and 20–25 ppt, pH 7.2–7.6, ammonia nitrogen below 0.2 mg/L, and chlorophyll-a below 10 μg/L. This study confirms that the two-stage GAM effectively overcomes the interference of zero-inflated data commonly encountered in larval fish surveys and can accurately reveal the response relationships between larvae and environmental factors. Based on these findings, it is recommended to prioritize the protection of mangrove edges and submerged vegetation areas while implementing ecological restoration and disturbance control measures. Additionally, enhanced regulation of ammonia nitrogen and chlorophyll-a thresholds during the rainy season is advised, along with the establishment of seasonal fishing bans from June to August. These measures aim to improve habitat quality and promote the sustainable recovery and conservation of early fish resources in the Wanquan River estuary.