Background: To investigate the trend of improper fund labeling and analyze the phenomenon of multiple annotations in one paper. Methods: A systematic sampling method was adopted to select academic papers from 23 medical university journals in the first issue of 2020 and the first issue of 2023. Each paper was screened, and the journal, number of issues, title, keywords, authors' names, their affiliated units, and approval numbers of all funding projects were recorded. Data of various projects of the National Natural Science Foundation of China (NSFC) were also extracted: Names, keywords, start and end dates of its projects; names of project leaders and participants; names of the applying units; completion status; and thesis titles. Results: The sampling method yielded 1090 sampled papers, 2014 funding projects, and 916 (84.04%) papers that received funding, with an average of 1.85 funded papers. A total of 392 papers had received support from 507 projects by the NSFC. Among the 2014 funding projects, 73.6% were labeled with appropriate timing, 7.7% had inappropriate timing, and 18.7% required clarification about whether there was any inappropriate timing. Twenty-one funding projects (1.0%) were approved for more than 10 years. The number of improper labeling of funding time in the first period of 2023 significantly decreased since 2020 (2.48 ± 1.44 vs. 4.35 ± 3.13, P < 0.001). Out of the 507 projects of the NFSC, 373 (73.6%) had content annotations that complied with regulations, 114 (22.5%) had no content annotations, 5 (1.0%) had no author annotations, and 15 had annotations that do not exist (2.9%). Conclusion: Improper funding labeling occurs in medical university journals. Relevant departments should take certain measures to curb the chaos in fund labeling. This is of great significance for maintaining academic integrity, clarifying the ownership of intellectual property rights, standardizing the use of funds, and improving the effectiveness of funding.

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