Abstract: Against the background of sluggish global economic recovery and " double down” of foreign trade in recent years, efficiency determines the development of ports as an important part of the global supply chain. Applying the panel data derived from 9 ports in the Pearl River Delta region from the year of 2010 to 2014, the efficiency of the Pearl River Delta ports is empirically analyzed by conducting the three-stage DEA model. The results indicate, (1) that the comprehensive efficiency of ports in Pearl River Delta region is low; (2) that the low comprehensive efficiency is attributed to the scale inefficiency; and (3) that the comprehensive efficiency, pure technical efficiency and scale efficiency of the port in the Pearl River Delta region have been increasing in recent years, but the rise is relatively small.