Objective Based on the triple perspectives of carbon source, carbon sink and non-point source pollution in the process of agricultural production, to measure the agricultural total factor productivity of Guangdong Province, scientifically grasp the basis of high-quality development of agriculture in Guangdong Province, and promote rural revitalization.

Method The DEA-Malmquist model was used to effectively measure agricultural total factor productivity in Guangdong Province from 2006 to 2021 and analyze its spatio-temporal differences, meanwhile the panel regression model was used to explore the influencing factors.

Result From 2006 to 2021, the agricultural total factor productivity of Guangdong Province was in an overall growth trend, with an average annual growth rate of 1.7%, although there were some inter-year fluctuations. The difference of agricultural total factor productivity in 21 prefecture-level cities in Guangdong Province was obvious, among which the highest was 1.070 in Zhuhai and the lowest was only 0.988 in Chaozhou. The region difference was presented in “Pearl River Delta region > Western Guangdong region > East Guangdong region > Northern Guangdong mountainous region” pattern. Technological progress was the key to the growth of agricultural total factor productivity in Guangdong Province. The urbanization level and agricultural industrial structure were the main factors affecting the agricultural total factor productivity in Guangdong Province.

Conclusion In order to improve the agricultural total factor productivity in Guangdong Province, it is suggested to increase the investment in agricultural science and technology, strengthen the popularization and application of green agricultural science and technology, optimize the financial support mechanism, vigorously cultivate and develop efficient three-dimensional ecological agriculture, and take the road of green agricultural development.