For the non-profit organization, data envelopment analysis (DEA) is one of the most effective methods for evaluating the performance. In this research DEA was applied to analyze the relative efficiency of six environmental agencies that have implemented the 10th five-year plan for Taihu Lake water pollution control in 2001-2005. The results show that technical efficiency and scale efficiency are unsatisfatory because 40% and 36.7% decision measurement units are of relative efficiency, respectively. Thus, nearly 60% decision measurement units should be regulated, and the functional relation between input and output should be recognized. For the external factors, significant difference is observed between the enterprise number and overall efficiency, but no significant differences among population, economic development level and overall efficiency. These results lead to suggestions to the environmental agencies on how to improve the implementation efficiencies.