In the strategic background of achieving a high level of self-reliance and strength in science and technology, the importance of technological innovation has been constantly highlighted. In practice, innovation activities have always been faced with dilemmas such as long R&D cycles, R&D risks and knowledge gaps. Individual innovation entities often struggle to achieve breakthroughs in research and development. As a result, cooperative innovation among enterprises, universities, research institutions, and governments has become more common. In recent years, the Central Committee of the Party and the State Council have paid high attention to cooperative innovation. However, existing studies from the perspective of fiscal and tax policies have mainly focused on the impact of government subsidies on enterprise cooperative innovation, with relatively less attention paid to the influence of external tax administration on this process. Using the data of China’s A-share listed companies from 2009 to 2022 and the quasi-natural experiment of the merger of the National Taxation Bureau (NTB) and Local Taxation Bureaus (LTB), this paper empirically explores the impact of the merger of NTB and LTB on enterprise cooperative innovation with the difference-in-differences (DID) method. To begin with, the findings indicate that the merger of NTB and LTB significantly promotes the level of enterprise cooperative innovation, and this core conclusion also holds even after several robustness tests, including parallel trend test, PSM-DID test, replacement of dependent variable, deletion of specific samples, eliminating the interference of other policies, modifying fixed effects, changing regression method and placebo test. The mechanism analysis indicates that the merger can promote enterprise cooperative innovation through three pathways: enhancing corporate commercial credit, improving corporate reputation, and increasing corporate risk-taking levels. Further heterogeneity analysis reveals that the merger has a more pronounced effect on cooperative innovation for large enterprises, high-tech industry enterprises, and enterprises in regions with high levels of legal systematization. Compared with the existing literature, the contributions of this research are listed as follows. First, from the special perspective of independence of tax collection and administration, this study explores the impact of the merger of NTB and LTB on enterprise cooperative innovation, thus enriching and deepening the research on the economic effects of external tax collection and administration on micro enterprises. Second, in terms of the mechanism test, this paper examines three mechanisms from the perspectives of commercial credit, corporate reputation and corporate risk-taking, which helps to comprehensively and deeply understand the positive role of the merger of NTB and LTB on enterprise cooperative innovation. Third, in terms of the heterogeneous test, from the perspectives of enterprise scale, enterprise industry and regional level of legalization, this study further verifies the heterogeneous impact of the merger of NTB and LTB on enterprise cooperative innovation, which provides empirical references and policy implications for tax collection and administration to promote enterprise cooperative innovation accurately and efficiently. This research reveals the internal logic of the positive impact of the merger of NTB and LTB on enterprise cooperative innovation to a certain extent. It also provides important policy insights for the continuous deepening of tax administration reform by government departments in the future to promote enterprise cooperative innovation. The policy recommendations are specifically manifested in the following three points: First, it is necessary to maintain the vertical tax administration system and reasonably adjust institutional settings. Second, the capacity to obtain tax-related information should be enhanced, tax service quality should be improved, and the corporate governance function of tax administration should be valued. Third, differentiated policy effects should be emphasized, and the coordination and cooperation among policies should be strengthened.