The Third Plenary Session of the 20th Central Committee of the Communist Party of China has proposed to promote the deep transformation and upgrading of industries, and pay attention to improving the tax system conducive to high-quality development and optimizing the tax structure in deepening institutional reform. Have tax and fee cuts promoted the deep transformation and upgrading of the industrial structure, and can they promote the high-quality development of the industrial structure? From theoretical level, this paper clarifies the direct impact, impact mechanism and environmental heterogeneity analysis of tax cut policies and fee reduction policies on high-quality development of industrial structure, in addition, it clarifies the synergistic effect of relevant tax policies and tax cut and fee reduction policies, and conducts empirical research using the panel data of prefecture-level cities in China from 2006 to 2022. The research results show that the tax and fee reduction policies ultimately promote the high-quality development of regional industrial structure through the three mechanisms of accelerating capital return, stimulating innovation vitality and stabilizing market expectations. After a series of robustness tests, this conclusion is still valid. Heterogeneity research shows that in regions with stronger local administrative protection and more rigorous tax supervision, tax cut policies are more conducive to the high-quality development of the industrial structure. Conversely, fee reduction policies do not exhibit significant differences in their impact on the high-quality development of the industrial structure, which may be related to the measures of fee reduction policies and the reduction mechanism. In addition, tax reform and tax cut and fee reduction policies have played a synergistic role, and they have a positive promoting effect on the high-quality development of regional industrial structure, indicating that combined tax policies can play a synergistic effect of policies and jointly promote the high-quality development of industrial structure. Finally, based on different tax reduction intensity, optimization of local tax environment, tax system reform and tax preferential policy coordination, the paper puts forward some policy suggestions on tax cuts and fee reductions. The paper thoroughly analyzes the differentiated impacts of combined tax reduction and fee reduction policies on the high-quality development of regional industrial structures, providing more detailed empirical evidence for the precise formulation of structural tax reduction policies. In terms of research methodology, a mechanism analysis framework encompassing capital reflux, innovation vitality, and market expectations is constructed. This not only reveals the pathways through which tax cut and fee reduction policies affect the high-quality development of regional industrial structures, but also delves into their underlying mechanisms. Through such multi-dimensional analysis, a more comprehensive understanding of the economic guidance effects of tax cut and fee reduction policies can be achieved, promoting the optimization and upgrading of industrial structures, and better leveraging the positive role of these policies in driving the high-quality development of industrial structures. Moreover, from the perspective of the entire process of policy implementation, the heterogeneous impacts of local tax administrative protection and tax collection intensity on tax cut and fee reduction policies are explored. This provides a reform direction for tax authorities to better exert the economic empowerment of tax system reform and improve local tax services. Finally, by integrating the synergistic effects of tax departmental system reform and tax cut and fee reduction policies, a solid theoretical basis is provided for the establishment of a multi-departmental collaborative cooperation mechanism by tax authorities.