Abstract: We propose the process model of web MIS based on MVC architecture,which can be used to describe the relationship and consequence of data transfer in different layers of MVC architecture.We also give the Petri net modeling steps of web MIS based on MVC architecture,which provides theoretical basis for analyzing,verifying and optimizing the business process of web MIS.Furthermore,we discuss the application of Petri net in system model-ing,taking scientific research MIS of Jinggangshan University as an example.The experiment and the analysis show that the Petri net modeling is feasible and effective on scientific research MIS.