Abstract: To address the issue of significant radial displacement fluctuations and instability of magnetic levitation molecular pumps at high rotational speeds, a method based on the rotor structure of the magnetic levitation molecular pump to suppress its radial displacement fluctuations is proposed. Taking a 1.5 kW, 27720 r/min high-speed magnetic levitation molecular pump as an example, a three-dimensional computational model is established. The finite volume method is used to solve the rotor rigid mode, bending mode, critical speed, and flexible support, determining the analytical relationship between the rotor radial displacement fluctuation frequency and the rotational speed. On this basis, the influence of changes in the magnetic levitation molecular pump rotor structure on its radial displacement fluctuations is analyzed and studied, revealing the mechanism affecting the radial displacement fluctuations of the magnetic levitation molecular pump rotor. The relationship between the frequency of radial displacement fluctuations and the axial length of the rotor is determined. Through comparative analysis of the radial displacement fluctuation tests of the developed prototype over the full speed range, the accuracy of the simulation calculations is verified. This method can suppress the radial displacement fluctuation frequency of the magnetic levitation molecular pump rotor above 80 Hz, providing a reference for the design of high-speed magnetic levitation molecular pumps.