Background <p>Migration, a widespread ecological phenomenon, significantly influences the spatial and temporal distributions of organisms by altering community structure and shaping food web dynamics and ecosystem functioning. In marine ecosystems, a combination of biotic and abiotic factors shapes species behaviors, reproductive patterns, and phenological traits, ultimately driving seasonal adaptive migrations across habitats. Throughout this process, shifts in species composition and resource density can not only modify the structure of trophic networks but may also lead to functional changes within the ecosystem. However, our understanding of how the adaptive migration of fish at relatively fine temporal scales in subtropical coastal waters affects food webs remains limited. This study employs regional-scale ecosystem survey and high-resolution trophic interaction data, constructing a comprehensive metaweb and seasonal subnetworks of the Beibu Gulf ecosystem, while applying topological network analysis and energy flux modeling to quantify how adaptive fish migration reshapes food web structure and energy flow dynamics.</p> Results <p>We found that the adaptive migration of fish in the Beibu Gulf enhanced connectivity between regions and caused community boundaries to shift northward along environmental isoclines, which results in the increased structural similarity of subnetwork among these regions. Simultaneously, this migration altered the community structure of fish within regions and led to spatial and temporal variability in fish species diversity and biomass. Although the increase in fish species diversity increased the complexity of the subnetworks, it did not fundamentally alter the topology of the subnetworks within the region or diminish the modularity of reconnected networks. Changes in species biomass transformed energy flux pathways in the northern Gulf from two pathways, which are dominated by benthic detritivore flows and pelagic phytoplanktivorous flows, to a single pathway that is predominantly reliant on benthic detritivore flows, whereas the energy flux pathways in the southern Gulf exhibited the opposite trend. These results suggest that natural boundaries formed between submodules, the trophic structure within these modules, and the consistency of the topological roles of certain super-generalist fish species contribute to the stability of the food web structure in the Beibu Gulf. Furthermore, changes in species biomass may have altered the relative utilization of resources by consumers across different habitats or the relative availability of these resources to consumers, and thereby affects the intensity of interactions between consumers and prey and potentially alters the pathways of energy flux transfer.</p> Conclusions <p>Our study examined the effects of seasonal environmental changes on fish migration and their subsequent impact on the structure and function of food webs in subtropical coastal waters. This research offers new perspectives on how global climate change may drive species migration, trigger food web reorganization, and induce cascading effects. Furthermore, the findings provide compelling evidence for prioritizing the monitoring of super-generalist fish species and adopting food web structural indicators in marine ecosystem management.</p>