According to theory of composite system, water resources sustainable utilization is composed of some subsystems including water resources, socioeconomy and environment. Each sub-system contains numerous elements. This paper designs the hierarchy multi-indicators system of the sustainable utilization of water resources in the area of Pearl River Delta, and applies Main Component Analysis Method and Analytic Hierarchy Process to assess the sustainable utilization of the water resources in the area of Pearl River Delta. The integrated assessment result objectively reflects the sustainable utilization of the water resources in the area of Pearl River Delta .Based on the results, this paper puts forward some suggestions on the water resources sustainable utilization in the area of Pearl River Delta.