The evaluation of agricultural green ecological efficiency can reflect the capacity of agriculture for sustainable development and reduce the endogenous pollution caused by agricultural waste in order to alleviate the weakening of agricultural ecosystems. Taking the agricultural green economy as the research object, an evaluation index system based on the theories of green economic efficiency and economic growth for agricultural green ecological efficiency was constructed, and the impact mechanisms of specific indicators on agricultural green ecological efficiency were empirically explored. In addition, based on the data envelopment analysis (DEA) model, the overall agricultural green ecological efficiency of China from 2002 to 2021 was evaluated and the efficiency characteristics were analyzed from multiple perspectives. Then, the indicators of policy, finance, communication, society and other aspects were added in order to construct a comprehensive evaluation model of agricultural green ecological efficiency using a combination of DEA and a BP neural network, and the feasibility of the model was verified. The results indicate that the agricultural green ecological efficiency increased from 0.7340 in 2002 to 0.8205 in 2021, an increase of 11.78%. Additionally, the technological efficiency of China’s agricultural green ecological system did not show a very obvious trend of divergence. The results of the BP neural network were consistent with those obtained using DEA, and the overall evolution trend of the calculated BP neural network and DEA were mutually verified and integrated. The effectiveness and accuracy of the BP neural network was verified via a comparison with DEA.