Coral reef ecosystems have been documented under the influence of human stressors and climate change in the South China Sea. However, the ecological effects of coral bleaching are largely unclear in the region. In this study, the food web of the coral reef ecosystem at the Qilianyu cluster (Xisha Islands, the northern South China Sea) was modelled using Ecopath with Ecosim to predict the future state of the ecosystem under the impact of fishing and ocean warming combining recent in situ survey data. The results indicated that the coral reef ecosystem at the Qilianyu cluster is relatively immature, and dominated by bottom-up control. Ocean warming is expected to reduce the biomass of most functional groups, increase the strength of bottom-up control mechanism, and further increase the immaturity of the coral reef ecosystem at the Qilianyu cluster, especially under the high emission scenario (SSP585). Reducing fishing effort would mitigate the effects of ocean warming on biomass and ecosystem structure as indicated by the changes in the biomass of most functional groups, ecological indicators and trophic control indicators. This study revealed the complex impacts of fishing and ocean warming on coral reef ecosystems. These findings provide a process-based understanding of how coral reef food webs in Chinese marginal seas may reorganize under interacting climate and fishing pressures, and highlight the need to integrate local fisheries regulation into climate-adaptive, ecosystem-based management for South China Sea coral reefs.