This study aims to investigate the repercussions of urban industrial land misallocation on green total factor productivity (GTFP) within the context of China's Yellow River Basin regions. Utilising data from 99 prefecture‐level cities over the period from 2007 to 2020, the analysis reveals that the misallocation of urban industrial land exhibits regional variations and exerts a significant and persistent negative influence on GTFP, with notable regional disparities. Further analysis shows the mechanism of this effect is the obstacle to urban innovation due to industrial land misallocation. In addition, education expenditure plays a moderating role both directly and indirectly. These findings imply the need to continuously improve the performance evaluation and financial system of local governments, reduce government intervention, and make use of the market mechanism in the allocation of urban industrial land.