Abstract: When the magnetic agitator is stirring, the radial runout of the stirring blade tends to be larger, which affects the stirring effect of the material and reduces the service life of the agitator. Therefore, based on the existing equipment, a three-dimensional model of magnetic drive agitator was established, and the radial stiffness properties of the magnetic drive agitator was simulated and analyzed by the Optistruct and Romax finite element analysis software. The influence of the bearing configuration on the radial stiffness of the agitator was studied. It was found that two types of bearing configuration were used between the spacer ring and the outer permanent magnet base. The second configuration is a pair of 6005 deep groove ball bearings, and the first one is a combination of a 6005 deep groove ball bearings with a 3204 double row angular contact ball bearings. The optimized bearing configuration was the first configuration. Compared with the second configuration, the radial displacement at the end of the stirring shaft was reduced by 26.9%. The influence of the thickness of the isolation ring on the maximum displacement, stress and modal of the mixing shaft was analyzed, and the reasonable parameters of the isolation ring wall thickness were obtained.