This report explores the change trends of and structural characteristics of the material flows of China’s special economic zones during 1996-2018 and studies the differences in resource efficiencies of and the situations of sustainable development of China’s special economic zones，through the material flow analysis. As shown in the studies，the growth rate of direct materials input （DMI） in Hainan was relatively stable，while other special economic zones show fluctuating DMIs；per capita DMI in Xiamen and Shantou remained basically flat during 2015-2018；the per capita resource consumption of Shenzhen showed negative growth，manifested by the falling trend of per capita DMI during 2008-2018；while Zhuhai’s resource productivity maintained steady growth. Shenzhen basically showed the low input/high output effect，with its resource productivity ranking first. Although the economic and material resources input by the five special economic zones showed a relatively slowdown trend，their ecological environmental carrying capacities still confronted certain pressure；the growth of resource productivity still can’t meet Pearce conditions，and the balanced development of population，resource and environment had not been realized. The material flow analysis method has certain application values in the researches on the resource efficiency evaluation and sustainable development；while a “resource-environment” assessment system should be built for the further researches on the sustainable development.