The reduction of individual tax burden and the overall increase in tax revenue are important issues in national governance, and their implementation requires effective guidance of corporate tax behavior as a key lever. The State Council has released Opinions on Further Optimizing the Business Environment and Reducing Institutional Transaction Costs for Market Entities. The reduction of institutional transaction costs can improve taxpayer satisfaction, strengthen tax collection and payment cooperation, and thereby enhance corporate cooperative tax compliance. However, existing research mainly focuses on the overall tax compliance of enterprise, and has not yet delved into the potential influencing factors of cooperative tax compliance. From the perspective of behavioral public finance, this paper takes corporate cooperative tax compliance as the entry point, separates the mandatory tax compliance part based on the A-S model, and constructs cooperative tax compliance indicators. It characterizes business environment innovation through the pilot program for business environment innovation, theoretically analyzing and empirically testing the impact of business environment innovation on cooperative tax compliance, as well as its underlying mechanism. The study finds that business environment innovation promotes cooperative tax compliance, which is further manifested in the fact that business environment innovation reduces the actual tax burden of enterprises and improves the overall tax contribution of the region. Mechanism testing reveals that business environment innovation incentivizes cooperative tax compliance by reducing institutional transaction costs. Combined with psychological theories and sociological theories, the study finds that the reduction of institutional transaction costs can enhance taxpayers’ tax morality, tax trust, and group identity, which is manifested in the fact that when the intensity of tax enforcement is lower and the ethical level of enterprises is lower, the promoting effect of business environment innovation is more significant, and enterprises in business environment innovation pilot areas exhibit a peer effect. This paper examines the impact of business environment innovation on corporate cooperative tax compliance from a new perspective of “public service” innovation, more comprehensively revealing the operational mechanism of business environment innovation. The findings have important policy implications for “creating a first-class business environment that is market-oriented, rule-of-law-oriented, and internationalized”.