Abstract: 【Objective/Meaning】With the reform of three subsidies in agriculture, the financial structure has changed. Exploring how the subsidies of farmland productivity protection affect the changes of total factor productivity in agriculture is helpful to improve the subsidy policies and provide reference and inspiration for promoting the agricultural development in Fujian Province. 【Methods/Procedures】By using the DEA-Malmquist model, the total factor productivity of agriculture in Quanzhou City, Ningde City and Zhangzhou City was calculated, and then the Tobit model was used to make regression analysis on the total factor productivity of agriculture. 【Results/Conclusions】The results showed that the technical efficiency was the main reason for the increase of agricultural total factor productivity. From the perspective of the influencing factors of agricultural total factor productivity, the subsidies for the fertility protection of cultivated land and the annual sunshine duration had significant positive impact on the total factor productivity of agriculture. The GDP of each county and city, the average cultivated area per household, and the annual average temperature had significant negative impact on the total factor productivity of agriculture, while the annual rainfall was negatively correlated with the agricultural total factor productivity.