In order to establish optimal clinical solution and speed up clinical pathway system construction, a modeling method using hierarchical timed colored Petri net (HTCPN) was put forward, thus clinical status, information flow as well as the relationship between clinical activities can be visually controlled. With the designed SML functions, realtime input is available for diagnostic decision and checking information. Parameters and conditions are set up to forecast and analyze variations in diagnostic processes, also automotive adjustment is able to be implemented. Using defined time stab of tasks, simulation analysis is conducted for different distributions of patients’ arrival rate, and then methods for resources allocation are proposed to improve the effectiveness of clinical pathway implementation. The test results confirm that this method is effective in solving current clinical problem, and it paves the way for developing clinical pathway workflow system.