The influence of land granting on green total factor productivity (GTFP) and its mechanisms remain under-explored. Based on dynamic spatial panel data of 30 provincial administrative regions in China from 2007 to 2017, this study attempts to establish the framework of a transmission mechanism among land granting, manufacturing agglomeration and technological innovation, and green total factor productivity, and measures their interactions by the mixed directional distance function and Global Malmquist–Luenberger index model containing undesirable output. Then, this paper empirically estimates the impacts of land granting, industrial agglomeration and technological innovation on green total factor productivity in China with a dynamic spatial mediating effect model. The results show that the development paradigm of China’s industrial green economy is characterized by path dependence, and industrial GTFP has a significant spatial effect. Local governments rely on low-price competition to obtain cost advantages and facilitate the agglomeration of local manufacturing industries, and promote the impact of negotiation on industrial GTFP through the mediating effect of manufacturing agglomeration. There exists a non-linear relationship between manufacturing agglomeration and industrial GTFP. The land acquired through negotiation has a promoting effect on green technology innovation, and will foster industrial GTFP through the intermediary effect of technological innovation. No obvious non-linear relationship is observed between technological innovation and industrial GTFP. The grant of “Tender, Auction and Listing” has no significant influence on the industrial GTFP, and the mediating conduction effect on the GTFP of industry is not established. Industrial structure, government management and infrastructure will significantly promote the improvement of industrial GTFP, while the level of transportation will inhibit the improvement of industrial GTFP. Through administrative intervention in low-production capacity departments, local governments can integrate regional resource endowments, give play to the comparative advantages of industries, and achieve industrial structure upgrades and core competitiveness, which will be conducive to the improvement of industrial GTFP. High-level transportation conditions increase energy consumption and greenhouse gas emissions in transportation operation, which makes no contribution to the enhancement of industrial GTFP.