The adjustment of agricultural economic structure under environmental change has become a key path to realize sustainable agricultural development. The purpose of this paper is to construct an analytical model to provide theoretical basis and practical guidance for agricultural economic restructuring. The model reflects the dynamic process of agricultural economic restructuring under environmental change by introducing indicators such as environmental technology efficiency and green total factor productivity. The model adopts the SBM directional distance function (SBM-DDF) and combines it with the Malmquist-Luenberger (ML) productivity indicators to measure the intertemporal dynamic changes of environmental technical efficiency and green total factor productivity in Chinese agriculture. The empirical analysis shows that the effect of environmental regulation on agricultural productivity in China has a distinct geographical nature. Currently, the environmental regulation construction in Chinese agriculture is relatively weak in general, and there is a great potential to improve the technical efficiency of agriculture, and the western part of the country should be a key area of concern for the future construction of environmental regulation in agriculture.