This paper constructs a threshold regression model to empirically test the non-linear relationship between rural human capital and agricultural green total factor productivity (AGTFP) with provincial panel data during 1993–2018. The results show that there is a significant double threshold effect between rural human capital and AGTFP under different levels of agricultural material capital (AF)and agricultural economic development (AGDP). When AF and AGDP are at different levels, the relationship between rural human capital and AGTFP presents an inverse N-type trend or an inverted U-type trend. The nonlinear relationship between rural human capital and AGTFP has been verified. It is necessary to attach importance to the promotion of agricultural human capital to the growth of AGTFP. It is suggested to strengthen education on environmental protection and green production technology training for farmers, and urge them to widely adopt the production mode of mitigating climate warming. In addition, it is important to ensure the coordinated development of AF and rural human capital while enhancing the input of AF.