The special financial funds of administrative institutions are special funds set up by the government to promote the development of specific undertakings and achieve specific goals. However, in recent years, the problems existing in the audit of financial special funds in administrative institutions in China, such as unscientific and unreasonable fund distribution, non-standard fund management, imperfect budget preparation system and low comprehensive quality of auditors, have become increasingly prominent, which seriously affect the efficiency and effect of the use of financial special funds, and also cause a waste of social resources. This paper aims to deeply analyze the problems existing in the audit of special financial funds in administrative institutions, and put forward corresponding suggestions for improvement, so as to better play the value creation role of audit supervision in the field of special financial funds.