The problem of environmental pollution is becoming more and more prominent. Making ecological governance take an effective and sustainable development path has become a complex problem for countries to think about. The proposal of green governance provides new ideas for governments to manage enterprises and local environmental governance. The DEA method is commonly used to measure the effectiveness of environmental governance, but the traditional DEA method ignores environmental factors and management factors, and the measurement error is significant. Therefore, this paper introduces the total waste discharge and PM2.5 average concentration and other unexpected outputs, using the three-stage DEA model and three-stage DEA Malmquist index model, creatively constructing the green governance measurement index system, which measures and evaluates the green governance efficiency of 30 provinces in China from 2004 to 2019 from static and dynamic perspectives. The research results show that the efficiency value obtained by the three-stage DEA model is higher than the first stage, which confirms that the external environmental factors have a specific impact on the GGE. At the same time, the comprehensive technical efficiency value presents a "U"-shaped trend with time. From the perspective of sub-regions, there is heterogeneity in the efficiency values between regions, showing a decreasing trend of "east, west, and middle." From the efficiency decomposition results, the main reason for the negative growth rate of GGE is the low efficiency of technological progress, which provides targeted suggestions for governance in various regions of China. This study will help provinces prepare to strengthen investment in technological innovation, maximize the benefits of input and output, and promote green and sustainable development.