In this paper, the rationality of Electromagnetic Compatibility（EMC）design of Printed Circuit Board (PCB) is evaluated in advance through electromagnetic simulation. The purpose of this method is to reduce the chances that the Electromagnetic Interference (EMI) of PCB does not meet GMW 3097 standard in EMC test. Firstly, the 3D electromagnetic field simulation of the Peripheral Component Interconnect express (PCIe) module on the PCB is performed. Then the field simulation is dynamically linked with the circuit simulation of the Simulation Program with Integrated Circuit Emphasis (SPICE) model of chip on the PCIe module, so that the co-simulation of field and circuit is performed. According to the experimental test, the accuracy of this simulation method is within 6 dBμV, which satisfies the deviation of PCB processing technology and the uncertainty of the experimental test. Thus, this simulation method meets the accuracy requirements. Therefore, the EMI of PCB can be evaluated and the PCB design can be optimized by this simulation method. After the 33 Ω resistors on the PCIe module was replaced by magnetic beads, the EMI of the PCB at 1.6 GHz is reduced by 13.4 dB. According to the 1-m method specified in the CISPR 25 standard for testing, the EMI of PCB becomes ?3.4 dBμV, which is lower than the GMW 3097 standard requirement. Therefore, the effectiveness of this measure is verified.