Small-scale fisheries (SSFs) play a vital role in the sustainability of local economies. Migratory species moving into and out of an ecosystem may influence the dynamics of local fish communities and SSFs. We used the end-to-end model, OSMOSE-JZB (Object-oriented Simulator of Marine ecOSystEms), to evaluate the impacts of fishing and a migratory shrimp (Trachypenaeus curvirostris) on the ecosystem of Jiaozhou Bay, China. Increased fishing intensity (i.e., annual fishing effort) resulted in the decline of four ecological indicators, including the total biomass of the community, mean trophic level of the community, inverse fishing pressure, and large fish index. Compared to managing fish stocks under uniform fishing mortality over the fishing season, landings and community biomass were higher when a “race to fish” (i.e., large catches in a short period) occurred. The results suggested that managing fishing seasonality (i.e., temporal allocation of fishing effort) could mitigate the negative impact of fishing intensity. Two resident high-trophic-level fishes were sensitive to changes in fishing intensity and fishing seasonality. The changes in trophic interactions had larger impacts on species at low trophic levels than fishing. Pearson's correlation analysis showed that T. curvirostris biomass was negatively correlated with the biomass of resident species and positively correlated with the biomass of other migratory species. We also found that fishing changed the impact of varying T. curvirostris migratory biomass on other species. Resident species were more sensitive to changes in fishing and T. curvirostris migratory biomass than other migratory species. We argue that SSFs management can benefit from the development of temporal fishing strategies and consideration of trophic interactions stemming from migratory species dynamics.