The agricultural environmental efficiency which combines both economic and environmental performance is of great significance to the efficient utilization of agricultural resources. Taking 30 provinces (cities and districts) in China as the research object, this paper used SBM (Slacks-based model) model, spatial Markov chain, GIS technology to depict the spatio-temporal evolution characteristics of agricultural environmental efficiency, then analyzed the influencing factors by using spatial Durbin model. The results showed that:(1) The agricultural environmental efficiency based on the non-expected output was lower than that without the non-expected output, which presented a continuous upward trend. The regional difference indicated an overall inverted V trend, the agricultural environmental efficiency decreased in the east-west direction, and the south-north direction showed a U shape pattern. (2) The different levels of the agricultural environmental efficiency had obviously spatial differences and spatial correlation characteristics. The geospatial structure played an important role in the spatio-temporal evolution and the spatial agglomeration was significant, and the evolution of different efficiency types had significant temporal and spatial inertia. (3) The agricultural environment efficiency had spatial spillover effects, the agricultural economic level, the environmental regulation and the agricultural production capacity played significant roles in improving the agricultural environmental efficiency, while the agriculture financial support, the industrialization level, the crop planting structure and the agricultural machinery strength would inhibit its development.