This article establishes an input-output index system based on DEA model, and then makes evaluation of ecological efficiency of 30 areas of China during the years from 1995 until 2007 by means of super efficiency DEA model. Finally, this article makes spatial difference analysis of the measuring results according to eastern, middle, western and northeastern region; meanwhile examine the convergence of the changing trend of ecological efficiency. The results show that the ecological efficiency of China during the years from 1995 until 2007 obviously represents regional differences and the rank ordering of average efficiency is as follows in turn: eastern, middle, northeastern and western region; the ecological efficiency of eastern, western and northeastern region presents the declining trend, while the middle region presents the increasing trend; the ecological efficiency of northeastern region exceeds the national average and all the rest of the ecological efficiency is below the national average. The conclusion can be drew from con convergence analysis that the national ecological efficiency assumes the lesser radiation trend during the years from 1995 until 2007, namely the gap of efficiency is gradually increasing, the main reason of which lies in the influence of ecological efficiency change of eastern region and smaller changes of other regions.