Keystone species play a critical role in sustaining ecosystem structure and function. Thus, accurately identifying keystone species is essential for effective biodiversity conservation. This study investigates the benthic ecosystem of Yanpu Bay’s mangroves, utilizing stable isotope analysis in combination with Bayesian mixture models and ecological network analysis to characterize trophic relationships and topological network structures, with the aim of identifying keystone species within the community. The benthic food web in this study comprised 96 connections and 27 nodes. Among them, Scartelaos histophorus preyed on eight benthos species, constituting 18.51% of the total prey sources in food web. Sedimentary organic matter (SOM) was identified as a critical food source, sustaining 17 consumer species, 62.96% of the total species recorded in the community. Quantitative analysis using criticality indices and key player problem indices identified Cerithidea cingulate, Littorinopsis scabra, Periophthalmus magnuspinnatus, S. histophorus, Bostrychus sinensis, and Metaplax longipes as keystone species. The identification of these keystone species provides valuable insights for developing targeted biodiversity conservation strategies and offers a robust scientific foundation for the restoration and sustainable management of the mangrove benthic food web.