The high-speed rotating superconducting rotor can be made into a high-precision inertial device. Centrifugal deformation is one of the key factors affecting the drift speed of the rotating superconducting rotor's polar axis. The larger the drift speed, the worse the accuracy of the inertial device. Applying magnetic torque to the superconducting rotor to compensate for the magnetic disturbance torque generated by centrifugal deformation is one of the effective methods to improve the measurement accuracy of the inertial device made of a superconducting rotor. To compensate for the magnetic disturbance torque caused by centrifugal deformation accurately, we studied the centrifugal deformation effect of the rotating superconducting rotor. In this paper, the centrifugal deformation of the superconducting rotor is analyzed first. And then the influence of centrifugal deformation of the superconducting rotor on magnetic force was studied by Finite Element Method (FEM). The results show that centrifugal deformation can reduce the magnetic levitation force of the superconducting rotor, leading to suspension position drift. Finally, the drift speed of the superconducting rotor's polar axis caused by centrifugal deformation is investigated, including the drift speed caused by centrifugal deformation of the rotating superconducting rotor, as well as the drift speed generated by the coupling of centrifugal deformation and suspension position drift of the superconducting rotor. The research results provide a reference for more accurate compensation of magnetic disturbance torque caused by centrifugal deformation and further improve the accuracy of superconducting rotor inertial devices.