The available sea surface temperature (SST) products are too coarse to assess the fine-scale (<1 km) SST variations related to coral bleaching. In this study, we proposed an optimal SST inversion model using Landsat 8 thermal infrared sensor (TIRS) images to derive fine-scale SST patterns in the coral reef habitats of the Xisha Islands, South China Sea. Our study included two parts: 1) six SST inversion models were developed using the radiative transfer method and the split window (SW) algorithm in the hot season and cool season, from which the optimal SST inversion model was determined; and 2) the optimal model was applied to 47 Landsat 8 TIRS images to derive the SST spatial and temporal pattern among the geomorphic zones of six reefs in hot and cool season conditions. Compared with the measured sea temperature data and the verified MODIS SST products, the SST6 model using the SW algorithm was optimal, with an RMSE of approximately 0.64°C in the hot season. The average SST results usually had a pattern of reef flat > lagoon > reef slope/offshore sea. The reef flat was usually approximately 0.05°C–0.2°C hotter than the lagoon in the hot season. The SST in the lagoon also increased from south to north and the shallow lagoon was usually warmer than the deep lagoon in the hot season. Our results suggested that scleractinian corals in the reef flat and the lagoon were more susceptible to bleaching-level thermal stress than other geomorphic zones. During the cool season, the SST fluctuated markedly among coral reefs and geomorphic zones.