Misconduct in funding acknowledgments in research papers has become a persistent problem in the field of research integrity. Its widespread and difficult-to-detect nature have attracted great attention from regulatory authorities and the academic community. Although a funding acknowledgment may appear to be ancillary information at the end of a paper, it directly affects the attribution of research outputs, the assessment of project performance, and the fair allocation of academic resources. Misconduct in funding acknowledgments not only distorts statistics on funded research outputs but also undermines the research integrity system, harming the research ecosystem and institutional credibility. Therefore, there is an urgent need to analyze the underlying causes and explore governance pathways. This paper analyzes research integrity misconduct case notices published on the official website of the National Natural Science Foundation of China (NSFC) from 2021 to 2025 and statistically examines cases involving improper acknowledgments of NSFC support. The results show that among the 314 papers involved in 132 cases of scientific misconduct, 282 papers acknowledged funding, encompassing a total of 201 funding sources. The proportion of funded papers was 89.8%. Improper acknowledgment involving multiple funding sources is a serious problem. Of the 282 funded papers, 106 (37.6% of the funded papers) acknowledged more than two funding sources, 28 papers acknowledged six funding sources, and 6 papers acknowledged seven funding sources. Among the 201 funding sources, 18 funding sources involved expired projects; 53 funding sources were acknowledged without authorization; four funding sources were unrelated to the paper; one funding source was fictitious; and two funding sources were recorded incorrectly. The paper delves into the underlying causes from four perspectives: institutional environment, subjective motivation, verification obligations, and regulatory technology. First, poorly designed evaluation systems (including academic evaluation and journal evaluation) is the fundamental incentive for misconduct in funding acknowledgments. Second, some researchers lack a strong awareness of research integrity or fail to clearly understand relevant regulations. Third, host institutions and journal publishers have not performed their management and oversight roles effectively or fulfilled their verification obligations. Finally, funding agencies have not provided convenient tools for project verification, and relevant definitions and rules remain unclear. Therefore, comprehensive measures are needed to address misconduct in funding acknowledgments in research papers. Following the logic of "source governance–process supervision–strict ex post punishment", this paper proposes a full-chain prevention and control system based on collaboration among multiple stakeholders, including NSFC, scientific researchers, host institutions, and journal publishers, to systematically curb misconduct in funding acknowledgments.