Strong EMI (Electro-Magnetic Interference) brings the problem of packet error and following retransmission. Especially in motion control area, the widely used Real-Time Ethernet SERCOS III will be seriously affected by EMI from the motor and other power electronic devices. This paper focus on the behaviors of synchronization mechanism of SERCOS III in a strong EMI environment. Strong EMI affect the precondition of SERCOS III’s synchronization mechanism, and the precision of synchronization is highly affected. A Timed Petri Net model of the former mechanism in packet error environment is created and simulated in the Timed Petri Net simulation software CPN TOOLS. The simulation results indicate that the synchronization error is up to about 0.5 to 45 times of retransmission cycle time. This error is unacceptable in motion control area. Then, the paper provides an improved synchronization mechanism, and similar simulation is run. Simulation results indicate that synchronization error is eliminated by the improved mechanism.