In this paper, a Colored Petri Net modeling method for early stage design of virtual assembly operation is presented. The characteristics of virtual assembly system, Petri Net and Colored Petri Net are analyzed. Some previous work in Petri Net application in assembly and virtual assembly system is discussed. The theoretical aspects of Colored Petri Net are introduced mathematically. Based on the mathematical presentation and the process of fasteners assembly operation, a Colored Petri Net model is constructed for the simulation of assembly operation in virtual environment. With CPN Tools software package, the simulation for evaluating the feasibility of modeling is implemented. It is demonstrated that the modeling approach can support the early stage design of virtual assembly system.