This paper proposed a clinical pathway Petri net model based on statistical αalgorithm, which integrate the basic Petri net with process mining algorithm based on statistical αalgorithm. This model can obtain medical procedure from event log and build clinical pathway Petri net model on the procedure. The medical procedure could be optimized and improved by analysis of the Petri net model. Simulation results shows that the statistical αalgorithm performs better in accuracy and efficiency than classic αalgorithm. The proposed model is verified on the real data of clinical pathway.