Abstract: Green certification is an important measure to promote the green transformation of agricultural enterprises and to advance the development of green agriculture. This article constructed a theoretical analytical framework for the impact of green certification on the technological efficiency of agricultural enterprises, and used 9 096 agricultural enterprises production data from 2013 to 2017 from China Academy for Rural Development-Qiyan China Agri-research Database (CCAD), Zhejiang University, to measure the technological efficiency. The time-varying Difference-in-Differences (DID) model and mediation effect analysis method were employed to empirically test the impact. The results showed that, (1) the average technical efficiency of agricultural enterprises in China was 0.392, which was still at a low level, and the efficiency of different types of enterprises , ranked from high to low, were production-oriented enterprises, processing-oriented enterprises and service-oriented enterprises. (2) Green certification had improved the technical efficiency of agricultural enterprises, with an increase of 8.4%. This impact still held true when considering the possible endogeneity and robustness tests. (3) The analysis of mediating effects found that green certification improved the enterprises’ technical efficiency mainly by alleviating information asymmetry, reducing transaction costs and increasing expected utility. (4) Heterogeneity analysis revealled that the impact of green certification on the technological efficiency of production-oriented and service-oriented agricultural enterprises was more significant, and its impact was greater in the eastern and western regions compared to the central region. Finally, this article proposed policy recommendations to enhance the technological efficiency of agricultural enterprises in China.