During the service process of bearingless motorized spindle (BLMS), its parameters change with time and external conditions, leading to the decrease in the accuracy of the motorized spindle. Therefore, it is difficult to accurately describe the dynamic performance of the motorized spindle during actual operation using deterministic parameters. In this paper, the interactions between thermal deformation and vibration of the motorized spindle are explored. The dynamic model of the motorized spindle based on multibody dynamics and time-varying parameters is established, and the solution method of dynamic model with uncertain parameters is investigated. Firstly, the reasons of vibration in the BLMS are analyzed, and the influences of thermal deformation on the thermal eccentricity and inhomogeneous air gap of BLMS are studied. The vibration model of the BLMS is established and solved to acquire the radial vibration displacement. Secondly, the discrete multibody dynamics model of the BLMS is built, and the center trajectory of the motorized spindle is attained by solving the multibody dynamics model. The prototype experimental platform of BLMS is designed and the vibration tests are carried out. The experimental results show that the vibration amplitude of the BLMS increases with the running time, and the maximum displacement has a large deviation from the simulation results using the determined parameters, while a small deviation from the simulation results using the uncertain parameters. It indicates that the solution of the multibody dynamics model of the BLMS described by uncertain parameters is closer to the experimental data. The research findings can provide reference for the optimized design of BLMS.