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With the world calling for environmental protection, China has to follow an innovation-driven development path in order to achieve its own high-quality and sustainable development. During this period, the problem of inefficient land use resulting from rapid progress in urbanisation is difficult to ignore. This study uses data from 30 provinces in mainland China to analyse the environmental protection effects of land use transition towards innovation-driven development, using spatial econometric models and entropy method. The results show that the innovation-oriented land use transition in four dimensions, human capital, material capital, urban function and government, is conducive to reducing industrial pollution emissions in the region, but this effect does not have a spillover effect. The results of this study provide some insights into the “triple-win” (environmental protection, innovation and land-use optimisation) approach to economic development in China.