Abstract:South China Sea is a significant area of global biological diversity. Due to the long-term unreasonable exploitation and utilization, the habitat there degenerates obviously, and the biodiversity loses seriously. The estimated annual loss of mangrove area ranges from 0.5% to 3.5%, and that of seaweed area is from 20%to 50%. A total of 82% of coral reefs in the Sea display evident degradation. In this paper, a trans-boundary diagnostic analysis of ecosystem degradation in South China Sea was conducted, with the focus on mangrove, seaweed and coral reef. Based on the analysis of the destruction state of the existing ecosystems as well as the main causes of habitat degradation and its trans-boundary impacts, some countermeasures on habitat conservation and management were put forward, aimed to promote the cooperation both at national and at regional levels to implement appropriate approach to reverse the ecosystem degradation trend in South China Sea.