Frequent occurrences of academic misconduct have become a significant obstacle to scientific progress, necessitating collaborative governance from multiple stakeholders to achieve effective mitigation. However, as pivotal institution in national innovation and the governance of academic misconduct, universities often neglect the issue of academic misconduct in promoting innovation. To elucidate the potential damage that neglecting research integrity governance may inflict on university innovation, this study utilized retraction and innovation data from Chinese Double First-Class Initiative universities between 2007 and 2017 to systematically (...) explore the impact, mechanism, and economic consequences of academic misconduct exposure on university innovation output. Our findings indicate that exposure to academic misconduct significantly reduces the innovation output levels of the involved universities, with research reputation being the primary mechanism driving this effect. The economic consequence analysis reveals that innovation stakeholders strategically adjust their behavior based on the research integrity status of universities. Such adjustments lead to a shift in research funding and innovation collaboration structures in a manner detrimental to long-term innovation, thereby causing economic losses to the universities’ innovation. Moreover, the negative impact of academic misconduct on university innovation output is more pronounced in STEM disciplines, comprehensive universities, and high-impact journal exposure events, and it intensifies with the prolongation of exposure lag time. Overall, this study enriches the theoretical framework of factors influencing university innovation output, clearly identifying the crucial role of research reputation in promoting university innovation. It provides theoretical basis and practical impetus for universities to proactively strengthen research integrity governance. (shrink)