Healthcare security system is one of the important mechanisms to ensure people's lives and health, and maintain social fairness and justice. As the main executor of the healthcare security system, medical insurance claim management and fund administration agencies bear important responsibilities in implementing medical insurance policies and benefits, managing the use of medical insurance funds, and regulating the behavior of designated medical institutions and drug stores. However, with the development of the social economy and the continuous deepening reform of the healthcare security system, the internal control management of medical insurance claim management and fund administration agencies still face many challenges and problems. Therefore, conducting in-depth exploration of the current situation of internal control management in medical insurance claim management and fund administration agencies and proposing corresponding reform measures has important theoretical and practical significance.