One of the main reasons for the inefficiency of environmental protection is the low efficiency of the use of financial funds.Based on environmental protection expenditure of 29 provincial governments in the mainland of China in 2015,this paper uses three-stage DEA model to evaluate the efficiency of environmental protection expenditure of provincial governments. The result shows that environmental protection efficiency in China is not high. And there are many differences in environmental protection efficiency among different regions. Environmental protection expenditure efficiency in east China is higher than that in central and west China. There are still large spaces to improve efficiency level in some arears. Then local governments should both enhance the management and optimize the size of funds to improve the expenditure efficiency. Fiscal decentralization,illiteracy rate and industrialization level all have negative effect on environmental protection expenditure efficiency,while economic development level and distribution density of environmental protection institutions have showed postive effect on expenditure efficiency. Based on pure technical efficiency and scale efficiency,environmental protection efficiency of local governments is divided into four types,and this paper proposes corresponding reform directions according to the features of different types.