Development of control model and system for FMS (flexible manufacturing systems) has long been interested by researchers. Presented in the paper is method for performance evaluation of FMS by using a new modeling tool which is called CTPN (Colored and Timed Petri Net). So, the procedure of modeling in the FMS is based on the IOM(Integrated Object-oriented Modeling) paradigm. A FMS, which consists of various machine groups, can produce machine parts in different physical dimensions and lot size. To model such a system, the method which utilizes CTPN is proposed. This enables the models according to part routings. The machine group which causes bottleneck is obtained and modified to relieve the problem. By iterating these steps which consist of modelling, simulation, and performance evaluation, a FMS canbe obtained which satisfies the required manufacturing conditions. Finally, The approach is the IOM from CTPN modeling by PNs and the other is a development of IOM tool for the performance evaluation of FMS.