Global coral reefs face severe threats from climate change and human activities, including marine heatwaves and overfishing of reef-associated fish species, heightens the risk of ecological phase shifts. However, significant uncertainty persists regarding the ecological health thresholds and dynamic evolutionary trends of coral reef ecosystems under various environmental pressures. Predictions of coral reef ecosystem dynamics are often hindered by sparse observational data. Ecosystem models provide valuable insights into future coral ecosystem dynamics, aiding coral ecosystem managers in decision-making processes. This study utilizes field measurements from coral reefs in the South China Sea, including Weizhou Island, Yongxing Island, and the Nansha Islands, to simulate the dynamic responses of coral reef ecosystems to persistent stressors such as regional ocean warming and overfishing of parrotfish. Findings reveal that, without accounting for thermal stress, the Nansha Islands exhibit considerable resilience, while Yongxing Island shows the lowest resilience. Parrotfish play a crucial regulatory role in coral reef ecosystems, and their susceptibility to fishing activities could lead to a gradual transition towards algal dominance, resulting in ecological phase shifts. The study recommends measures including the prohibition of parrotfish fishing, establishment of marine protected areas, and implementation of artificial breeding programs to sustain parrotfish populations in the South China Sea, thereby bolstering their crucial role in preserving the stability and resilience of coral reef ecosystems. The sea surface temperature response model predicts that coral growth rates initially rise with increasing sea temperature but declines after surpassing the optimal temperature, leading to ecological phase shifts and the threat of extinction for coral reef ecosystems. The low-latitude Nansha Islands are notably impacted by thermal stress, whereas the high-latitude coral reefs of Weizhou Island experience less thermal stress, potentially serving as future refuges for South China Sea coral reefs under high-temperature conditions.