Molecular pumps have been widely used in the vacuum metallurgy, coating, semiconductor manufacturing and many other fields in which the high vacuum, ultra-clean environment is needed. The application of magnetic bearings can bring many advantages for molecular pump, such as eliminating the friction, decreasing the power loss, lowering the maintenance costs, and increasing the rotating speed and service life. Besides, the magnetic bearings can fundamentally solve the vacuum chamber pollution problem which is caused by the backflow of lubrication oil steam. The three-pole magnetic bearings are the simplest structure of radial magnetic bearings and can be driven by three-phase converter which has the advantages of low costs, small volume and low power loss. In this paper, the performance of the three-pole active magnetic bearing (AMB) and hybrid magnetic bearing (HMB) are compared based on radial force–current characteristics analysis. Firstly, the mathematical model of three-pole AMB and HMB is built by equivalent magnetic circuit model, and the radial force–current characteristics are analyzed. Then, simulation by the three-dimensional (3D) finite element method (FEM) is performed. Finally, the experiment is conducted. The FEM results are consistent with the analytical results, showing that the nonlinearity and coupling of three-pole HMB are lower than three-pole AMB. The reason of causing nonlinearity and coupling is also discussed.