Coral reefs are one of the most important ecosystems on Earth due to their rich biodiversity and economic value. Since most coral reefs are far away from the mainland and underwater, remote sensing technology is an effective method to achieve real-time and large-scale monitoring of coral reef areas. However, the satellite monitoring and early alerting of environmental information such as thermal bleaching, water depth, and wave energy in coral reef areas, still have low accuracy. Taking South China Sea islands and near-shore coral reefs as the study area, we integrated technologies of remote sensing, geographic information system and wave simulation model to carry out the following research works: 1) Optimization the alerting thresholds of coral thermal bleaching in the South China Sea; 2) Spatial and temporal pattern analysis of coral thermal bleaching in recent 10 years; 3) Deriving fine scale patterns of sea surface temperature in coral reef habitats; 4) Optimizing active and passive satellite inversion model of water depth in coral reef area based on geomorphic segmentation; 5) Numerical simulation and spatio-temporal analysis of waves in reef areas based on SWAN modeling. The results of these studies can provide methods and theoretical support for large-scale coral bleaching monitoring and spatial pattern analysis of coral distribution.