To carry out pollution-free agricultural products certification work is the important issue of people’s daily lives. It is of great significance to construct the pollution-free agricultural regulatory system (PFARS) and achieve the office automation of the certification business. However, the PFARS contains much more steps in dispersion areas that it is very complex for business processes of E-PFAPC. In this paper, we not only provide the method of modeling the PFARS with Petri Net, but also provide the improved method to analysis the Performance of the constructed workflow model. The model for the PFARS provides a more simply process management than original work method. The provided workflow model analysis method can effectively verify the performance of building model. The results show that the PFARS system constructed by the workflow model can implement the business run automatically and own prefect performance.