The well-being of marine ecosystems significantly influences biodiversity and ecological equilibrium amidst pressing challenges such as overfishing, water pollution, and climate change. Drawing upon data from two fishery stock surveys conducted in the inshore waters of Hainan Island in 2022, this study undertook a comprehensive evaluation of the marine ecosystem’s health status in the region. Employing the Fish Index of Biological Integrity (F-IBI) analysis method, coupled with an examination of the structural and functional aspects of the fish community, our research sheds light on the prevailing conditions. Our study revealed a spatial dichotomy within the fish communities of the study area and delineated them into two distinct groups: the northwestern and southeastern ones, with evident disparities in community structure between the two. By employing indicator screening and calculation, we segmented the fish health index in the inshore waters of Hainan Island into five tiers. Despite discernible anthropogenic influences, the ecological health of these waters remained generally robust. Notably, the mean F-IBI of fall (56.30) significantly exceeded that of spring (48.16) (P < 0.01). Furthermore, regarding spatial distribution, the ecological well-being of the southeastern waters surpassed that of the northwestern and Qionghzhou Strait waters. This study represents a pioneer endeavor to apply ecological health assessment methodologies towards informing resource management and conservation strategies for the inshore fisheries of Hainan Island. By furnishing a scientific foundation, our research contributes to the pursuit of sustainable marine ecological development within this locale.