Under the global change, coral reef reserves pave an effective way to protect biodiversity and enhance coral reef resistance to climate warming. Moreover, maintaining coral reef resilience is the core of coral reef reserves. Based on thermal stress, which is the most serious factor of coral reefs, this paper builds a thermal stress intensity model adopting the satellite sea surface temperature data (SST) of the South China Sea from 1982 to 2009 and the predicted SST data of the Second Generation Canadian Earth System Model (CanESM2)in CMIP5 from 2006 to 2100. Coral reefs that have priority to be protected in RCP4.5 and RCP8.5 scenarios are distinguished from the view of maintaining their resilience. The results show that about 13% of the coral reefs in the South China Sea Islands are identified as priority areas for protection. Based on the relationship between thermal stress intensity and coral resistance as well as refugia, thermal stress intensities of Qilianyu and Jinqing Island in the Xisha Islands both in recent years and in the future are relatively low. Thus, they are recommended to implement complete protection policies after acting their service function. Dongsha Atoll of Dongsha Islands and Paihong Reef of Zhongsha Atoll have experienced serious acute thermal stress in recent years, for which 50% prohibition of protection are recommended. The acute thermal stress intensities both in recent observations and in future projections of Huangyan Island of Zhongsha Islands are relatively low. Fifty percent multi-purpose protection is recommended for Huangyan Island. About 14% of the coral reefs in the Nansha Islands are priority areas for protection, and 30%-100% for prohibition of protection or 30%-50% for multi-purpose protection can be implemented.The extracted reefs and the protection measures for the South China Sea Islands under the RCP4.5 and RCP8.5 scenarios can provide important reference value for maintaining the ecological resilience of coral reefs to cope with global climate change.