Aiming at the current situation that most hospitals still use private cloud with low computing resources, a medical big data processing system (BDPS) based on the workflow model is proposed and evaluated. Firstly, the contradiction between performance and cost in private cloud is studied. Secondly, the hybrid cloud is investigated to solve the above problems. Thirdly, a medical BDPS based on the workflow model is proposed, and the corresponding architecture and the workflow model are given also. The simulation results verify the rationality and validity of the proposed model.