The invention discloses an HIS based intelligent therapeutic drug monitoring whole process management system and a method thereof. The therapeutic drug monitoring whole process management system comprises a management control system, an HIS system, a TDM knowledge database, a prompt information base and a nursing workstation, wherein the management control system comprises a control module as well as an extraction module, a query module and a storage writing module connected with the control module, the output end of the HIS system is connected with the input end of the extraction module, the query module is connected with the TDM knowledge database and the prompt information base, the storage writing module is connected with the TDM knowledge database and the prompt information base, and the nursing workstation is connected with the control module. The system can effectively avoid the repeated detection of drug related genes, ensure the qualified rate of plasma concentration specimens, improve the working efficiency of the staff, and reduce the waste of medical resources fundamentally.