This paper used factor analysis method to establish the evaluation index system. We selected Shaanxi as the representative area in China, and used DEA-Malmqusit method to evaluate its governance and optimization efficiency of regional ecology economy system from 2004 to 2014. The output-SBM model was used to estimate the efficiency value for 31 provinces in China. The results show that the efficiency of the governance and optimization efficiency of regional ecology economy system in Shaanxi is declining. The efficiency values in Central and Western Province are much less than Eastern Province. For Eastern Province, forest volume and the proportion of a protected area output shortfall, while per capita water resource and industrial wastewater discharge output shortfall for Central and Western Province.