With the universal coverage of healthcare security and the improvement of medical technology, the expenditure of medical insurance funds has increased, and the illegal behaviors of medical institutions and drug stores have become more hidden. This paper expounds the current situation of the medical insurance audit management of retail pharmacies in Yi'an District, Tongling City of Anhui Province, analyzes the inspection methods of retail pharmacies over current problems, and puts forward countermeasures such as strengthening the audit, building an audit talent team, introducing third-party forces, and building an information-based and data-based medical insurance subsystem, in order to provide reference for the supervision of medical insurance funds of retail pharmacies.