An efficient and convenience model of business process plays a crucial role in scientific project management. Existing Petri net models lack the ability to cope with the time constrain of the business process. Thus the time factor was introduced to Petri net in this paper. The formal definitions of time Petri net were presented in details. The techniques to model the business process of scientific project management system with the time Petri net were discussed as well. A time Petri net model for an instance of scientific project management system was setup and study. The research results indicate the time Petri net is an efficient method to represent the scientific project management system.