The main helium fan is the key dynamic equipment in the primary circuit of high temperature gas cooled reactor, which is supported by electromagnetic bearing. In typical dynamic conditions such as valve opening adjustment, impeller speed adjustment, and loop resistance adjustment, the fluid pressure pulsation in the fan is significant. The fluid pressure pulsation acts on the rotor and thus affects the operation of magnetic bearing, while the control and adjustment of magnetic bearing changes the state of the rotor and thus affects the fluid pressure pulsation, which poses a challenge to the stable operation of the magnetic bearings as well as the main helium fan. In this paper, based on the Computational Fluid Dynamics (CFD) method, a high-fidelity transient computation of fluid pressure pulsation of the helium fan under the above typical operating conditions is carried out by using the SST k-ω model to obtain the excitation spectrum of the pressure pulsation. The closed-loop simulation system of magnetic bearing is established, the pressure pulsation excitation spectrum is used as the excitation source to stimulate the magnetic bearing system, and the response of the magnetic bearing system is obtained. The anti-disturbance ability of different control strategies and control methods is compared, which provides a basis for the control of stable operation of magnetic bearings under strong fluid pressure pulsations and a reference for the reliable operation of the main helium fan.