Abstract: There are a great number of DEA models proposed to deal with ecological efficiency problems with undesirable outputs. However, which model should be used in a specific scenario or how about the discriminability of a given DEA model is hard to decide in practice. This paper uses the ecological Shannon DEA procedure based upon the existing study to obtain an ecological comprehensive efficiency score for each decision units. The procedure is used to appraise the ecological evaluation to 32 paper mills along the Huai River in China. The results seem reasonable since they integrate the results of existing relevant DEA models, and calculate the importance degree of each model. The procedure can also be used to determine the pollutant emission quotas for those paper mills.