Scaled operation and green development are the essence of achieving high-quality agricultural development. Clarifying the relationship between scale operation and green agricultural development is of important theoretical and practical significance. The SBM-GML index was used to calculate and characterize the spatiotempora evolution trend of China’s agricultural green total factor productivity. Based on provincial panel data from 2008 to 2021 in China, a fixed effects model was used to empirically study the impact and pathways of land scale operation and service operation on agricultural green total factor productivity. Research has found that at the provincial level in China, the green total factor productivity and scale management showed an overall upward trend during the research period. There exists an inverted U-shaped non-linear relationship between land scale operation and service scale operation on agricultural green total factor productivity, which first expands and then decreases. The level of agricultural mechanization plays a role in the impact of scale operation on the green total factor productivity of agriculture. The effects of two kinds of scale operation on green total factor productivity of agriculture vary across different regions. Therefore, it is necessary to promote moderate-scale operation in agriculture, improve the level of agricultural mechanization, and develop scale operation tailored to local conditions.