Rational use of medicines is essential to safeguard patient safety and therapeutic efficacy. Drug instructions constitute the legal basis for medication use, while medical insurance reimbursement policies directly determine drug accessibility and financial burden. In recent years, with the continuous adjustment of medical insurance payment policies and the improvement of drug management regulations, the practical management of drug use in accordance with instructions and medical insurance payment restrictions in medical institutions has become a research hotspot. This review focuses on the current management status of drug use in accordance with instructions and medical insurance payment restrictions in medical institutions, deeply analyzes the existing problems and their interrelationships, and proposes optimization strategies for management. It aims to promote rational drug use in medical institutions, maximize the efficiency of insurance funds, protect patient rights, and ensure the stable operation of the medical system.