Objective: Misusing prohibited medications in clinical trials may lead to protocol violations and compromise patient safety. Clinical trial guidelines indicate that ensuring trial quality and medication control is essential. This project aimed to establish a patient-centered prohibited drug management system to improve data transparency, enable automated verification, enhance trial quality, and ensure patient safety. Methods: A problem-solving approach was used to identify seven root causes of prohibited drug processes in clinical trials. Four major countermeasure groups were established: standard operating procedures, batch uploads with data correction, three-level risk alerts with dual-code verification, and personalized control settings. Results: After implementation, the number of protocol violations attributable to prohibited drug use decreased from 18 to 0. The prohibited drug configuration completion rate increased from 20% to 100%, and the average documentation time reduced from 102 to 18 minutes. Both internal and external customer satisfaction exceeded 90%. Conclusion: The proposed system introduces systematic management capabilities and optimizes human–system interaction. Its successful implementation demonstrates strong potential for application across affiliated hospitals to further enhance medication safety.