Objective：To improve the internal audit quality and use efficiency of scientific research funds under the policy of “simplified regulation and optimizing service”. Methods：Data were collected on the implementation of scientific research funds in Shanghai TongJi Hospital in recent 5 years. Likert scale was designed to investigate the perceived status quo of the internal audit qual- ity of the hospital’s scientific research funds, and SPSS 25 was used to calculate the mean value and dimension reduction analysis. Results：The average implementation rate of total scientific research funding from 2017 to 2021 was 80.03%. The overall effect of in- ternal audit quality was optimistic (mean 4.48), while the score of J (4.38) and M (4.37) was low. Different groups have significant dif- ferences in the perception of internal audit quality. Conclusion：The overall perception of internal audit quality is good, the subject leaders pay more attention to the quality of internal audit, the budget and use management of scientific research funds are not stan- dardized, the correlation between audit results and performance is not significant, audit service awareness and audit execution efficien- cy still have space. A successful final-oriented “3+3” independent functional mechanism of internal audit should be established to refine and construct the fund risk control matrix, implement the data platform early warning measures, and link the quality perfor- mance of internal audit.