Industrial structure upgrading is a huge driving force for China’s green economic development. The Yangtze River Economic Belt (YREB), a crucial component of China’s spatial economic pattern, is facing the dual pressure of economic development and environmental protection. Therefore, it needs to have its industrial structure upgraded immediately. This article measures the development levels of green finance using the entropy method and bases its analysis on the panel data of 11 provinces (municipalities) in the YREB from 2005 to 2019. A moderated mediating effect model is then built to thoroughly examine the influence paths of green finance and green technology innovation on industrial structure upgrading. According to the empirical findings, green finance and green technology innovation have a significant direct role in promoting the upgrading of industrial structures. They reflect significant regional disparities across the East, Midland, and West. Second, green technology innovation has an effective transmission mechanism in green finance, boosting industrial structure upgrading. Third, environmental regulations positively regulate green finance’s direct and indirect routes to support industrial structure upgrading. This study is the first to combine green finance, green technology innovation, environmental regulation, and industrial structure upgrading under one research framework, broadening the research scope of industrial transformation. These research findings provide theoretical and practical guidance for upgrading China’s Yangtze River Economic Belt’s industrial structure.