With the application of digital technology, the digital industry has become a crucial engine driving industrial structure upgrading and high-quality economic development. At the same time, the increasing global resource and environmental pressure calls for environmental protection and sustainable economic and social development. Countries are committed to accelerating technological innovation, promoting the transformation and upgrading of economies, energy, and industrial structures, and improving green total-factor productivity, so as to achieve green production. In this context, the relationship between the digital industry and green total factor productivity has become one of the current research hotspots. Yet, most existing research focuses on the impact of the digital economy and digital technology on economic growth and industrial structure. Little research has been conducted on the relationship between the digital industry and green total factor productivity. This paper uses data from the China Statistical Yearbook, China Environmental Statistics Yearbook, and China Urban Statistical Yearbook compiled by the National Bureau of Statistics of China. The entropy weighting method is used to measure the comprehensive indexes of the development level of digital industries in 30 provinces in China. The level of green total factor productivity is calculated by constructing a super-efficiency model and using the SBM-DEA method. The relationship between digital industry development and green total factor productivity is empirically investigated using the panel fixed effect model and the mediation effect model. It is found that the development of the digital industry significantly promotes green total factor productivity, and resource allocation plays a transmission role between the two. That is, the development of the digital industry optimizes the factor allocation mode and improves the efficiency of traditional resource allocation, which in turn promotes the optimization and upgrading of industrial structure and green transformation, thus promoting green total factor productivity. Moreover, there are differences in the degree of impact of digital industry development on green total factor productivity under different productivity levels and industrial structure levels. This paper contributes to the existing literature in two aspects. Firstly, it investigates how the development of digital industries promotes green total factor productivity from an industrial perspective, unlike existing studies that focus on the digital economy level. Secondly, it not only explores the impact of resource allocation on green total factor productivity but also investigates the effect of the conduction mechanism that resource allocation produces between the development of digital industries and green total factor productivity. This paper further discusses the effects of different levels of productivity and industrial structure on green total factor productivity. Based on the existing “digital divide” and the reality of unbalanced regional development in China, this paper discusses the relationship between digital industry development and green total factor productivity. It provides theoretical support and policy recommendations for promoting the green transformation and green development of the digital industry and helps to promote the sustainable development of the economy.