Accelerating the green development of the dairy industry is an important work to promote the construction of ecological civilization and ensure the safe supply of dairy products. Existing studies lack a comprehensive analysis of the green development characteristics of China’s dairy industry. Based on the input–output system, the study measured and analyzed the green total factor productivity of China’s dairy industry in 29 provinces (cities, autonomous regions, and municipalities) since the 10th Five-Year Plan period, using the super-efficiency EBM model and the GML index based on non-directional and variable scale returns. Accelerating the green development of the dairy industry is an important work to promote the construction of ecological civilization and ensure the national nutrition intake. The existing studies lack a comprehensive understanding of the green development characteristics of China’s dairy industry. Therefore, this paper constructs an input–output system, measures and analyzes the green total factor productivity of the dairy industry in 29 provinces (cities, autonomous regions and municipalities directly under the Central Government), since the “15th Five-Year Plan” period based on the non-oriented super-efficiency EBM model and GML index with variable returns to scale. On this basis, the dynamic evolution of regional differences was explored using Kernel density estimation and the Dagum Gini coefficient, and the influencing factors of green total factor productivity in China’s dairy industry were analyzed using a two-way fixed effects model. The results show that from 2001 to 2020, the green total factor productivity of China’s dairy industry showed an overall upward trend, and presented a gradient pattern of “Northeast–East–Central–West” in turn, with green technical efficiency being the main driving force for promoting green total factor productivity in China and various regions. The gap in green total factor productivity between provinces and cities is gradually narrowing, and the polarization phenomenon is weakening. Super variation density is the main source of regional differences, and the difference between the West and the East is the largest, while the difference between the Central and the Northeast is the smallest. As for the influencing factors, industry agglomeration, economic development level, and environmental planning level have a significant positive promoting effect on the green total factor productivity of China’s dairy industry, while the level of population urbanization has a significant inhibitory effect on it. In order to promote the green and sustainable development of China’s dairy industry and promote the coordinated development of regional green, it is necessary to accelerate the efficiency of green technology while promoting the innovation of green technology, accelerate the integrated development of industry and formulate relevant policies according to local conditions to promote the coordinated development of green technology between regions.