The eco-efficiency and sustainable development have become the focus of world and the issues to be resolved urgently. In this paper, the recent research status of eco-economic region of Poyang Lake in China is analyzed, and the multi-level evaluation index system of eco-efficiency of Poyang Lake is constructed. The minimum input and maximum output method based on DEA(Data Envelopment Analysis) is proposed, the mathematical model of validity evaluation of eco-economic region of Poyang Lake is set up and programmed by MATLAB. Efficiency evaluation of a complex system with the cases from nine districts of Poyang Lake region in China is realized, which is more than one homogeneous decision-making unit of multi-input and multi-output. The MDEA (Modified DEA) method resolves the problems of ranking DEA efficient units of Poyang Lake, The DEAP2.1 software differentiates the technical efficiency and scale efficiency of eco-economic region of Poyang Lake, and adjusts the DEA inefficient units to become technical efficiency. The model can be used to analyze efficiency and diagnose different units at the same time or same unit at different time. It can be more accurate and convenient for the management process of eco-economic region of Poyang Lake and the similar eco-economic region.