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Hua Zheshen Ming Chen Baiyan Shao Yijie Liu Haoyuan Luo Sangzhaxi (Nanjing Audit University, Jinling College, Jiangsu Nanjing 210023) Abstract: Green taxation has been playing a significant role in China's economic development, promoting enterprise transformation and upgrading, and building a solid protection wall for green mountains and clear waters. Based on defining the green taxation system, this paper analyzes the mechanism of green taxation in promoting enterprise innovation and transformation, examines the challenges faced in its implementation, and proposes corresponding solutions. The research shows that green taxation incentivizes enterprises to engage in green technology innovation and industrial structure optimization by increasing pollution costs and providing tax incentives, thereby driving enterprises toward green and low-carbon transformation. Since the impact of green taxation varies significantly across regions, industries, and enterprise types, policy design must fully account for these heterogeneities to achieve sustainable economic, social, and environmental development. This study provides references for green taxation to better exert its guidance and regulation functions and optimize institutional design. Keywords: Green taxation; Enterprise innovation; Industrial upgrading Fund Project: National College Student Innovation and Entrepreneurship Competition Project "Research on the Effects of Green Taxation in Promoting Enterprise Technological Innovation and Transformation Upgrading—A Case Study of Resource-Based Enterprises" (No.: 202413994002Z)