The EBM model and the random panel Tobit model are used to measure the agricultural environmental efficiency of the nine cities in Fujian Province from 2000 to 2017, and to analyze the influencing factors of the agricultural environmental efficiency. The results show that the agricultural environmental efficiency shows a general downward trend in Fujian Province, and the differences between the regions are obvious. There is a "positive U-shaped" Kuznets curve relationship between the agricultural added value per capita and the agricultural environmental efficiency. The level of openness has a positive impact on environmental efficiency, while the level of industrialization,the income gap of urban-rural and the intensity of pesticide have a negative impact on the efficiency of agricultural environmental in Fujian Province.