By introducing development situation of specialized cooperatives and vegetable specialized cooperatives in China, this paper discussed existing problems in the process of development of China’s vegetable specialized cooperatives. Then, it made efficiency evaluation on typical vegetable specialized cooperatives in 3 districts of Chongqing Municipality by the DEA method. Considering traditional DEA model has drawbacks, it introduced super efficiency DEA model to make complete identification and ordering of cooperatives. On this basis, it divided efficiency value into pure technical efficiency and scale efficiency, and classified cooperatives into 4 categories according to efficiency characteristics of non-complete effective cooperatives. Finally, it came up with recommendations and countermeasures for improving efficiency of specialized cooperatives from raising technical level and increasing members of specialized cooperatives.