The maglev vehicle-guideway coupled system is a stochastic dynamic system with essential random vibration performance and has not yet been sufficiently studied. This study presents a three-dimensional (3D) maglev vehicle-guideway time-variant model to investigate the system's dynamic behavior. In this model, the 3D vehicle subsystem, comprising numerous components, is established. The 3D flexible guideway subsystem with uncertain parameters is developed using the finite element method. These subsystems are interconnected through interactive levitation and guidance forces regulated by the proportional-integral-differential controller. In addition, the probability density evolution method, combined with a generalized F-discrepancy representative point selection strategy, where the random irregularity and multiple uncertain parameters are considered, is employed to calculate the random lateral and vertical dynamic responses of vehicles, guideways, and electromagnetic forces. The mean values, standard deviations, and limit values meeting various probability guarantee rates are determined for different scenarios. An electromagnetic suspension high-speed maglev vehicle traveling on a simply supported guideway serves as a case study. The physical model is verified by measurement data. The accuracy and efficiency of this model are further assessed by the Monte Carlo method. The results indicated that the proposed model is practicable for random vibration analysis of maglev systems with considerable accuracy and efficiency. Finally, the impact of random irregularities, random Young's modulus, mass density, and damping ratio on the random dynamic responses are analyzed.