In the face of increasingly severe resource and environmental constraints, accelerating the transformation of agricultural green development through agricultural science and technology innovation is an effective measure to reduce agricultural pollution and improve agricultural production efficiency. From the perspective of multidimensional proximity, this paper expounds the mechanism of agricultural science and technology innovation on agricultural green development through spatial spillover from two perspectives: factor spillover path and product spillover path. Based on panel data of 30 provinces in China from 2006 to 2019, using the gray correlation analysis method, the level of agricultural green development in China was measured, and its spatial–temporal evolution trend was analyzed. The spatial economic matrix was selected as the spatial weight matrix, and the spatial econometric model was used to analyze the spatial spillover effect of agricultural science and technology innovation on agricultural green development. The results showed the following: (1) Agricultural green development had distinct spatial characteristics. The development level of green agriculture in eastern and northwestern China showed a trend of fluctuation decline, while that in southwest China showed a trend of fluctuation increase. The overall spatial distribution of green agriculture was high in the east and low in the west. (2) The spatial distribution of agricultural science, technological innovation and the agricultural green development level showed a significant positive global spatial autocorrelation, and the local spatial pattern characteristics of a number of provinces showed high-value agglomeration (HH), low-value agglomeration (LL), low-value collapse (LH) and high-value bulge (HL) as the auxiliary local spatial distribution. (3) Under the economic matrix, the improvement of the agricultural science and technology innovation level not only had a significant promoting effect on agricultural green development within each province but also promoted agricultural green development in neighboring provinces through positive spillover effects. This study provides insights that can help make up for the lack of regional agricultural science and technology investment, formulate scientific regional agricultural science and technology innovation policies and promote agricultural green development.