The quality consistence and machine utilization of a flexible manufacturing system (FMS) strongly depend on the statistical process control (SPC) and the correct fault diagnosis of equipment. An FMS can be modelled by the colored timed Petri net (CTPN). However, most CTPN models of FMS lack the activities of SPC and fault diagnosis, and they lead to incomplete FMS CTPN models. In this paper, the CTPN-based SPC and fault diagnosis models are proposed to model the FMS SPC and fault diagnosis behaviors. Since the models depend on the measured data from the inspection machines and the sensor data from the devices, the CTPN-based SPC and fault diagnosis models can be incorporated into the production CTPN models to give a complete model of FMS activities. It is shown that the CTPN-based fault diagnosis is easy to model, and the results are straightforward.