In order to reduce the vibration of mountain self-propelled electric monorail transporters (MSEMT) caused by the impact of the meshing of roller gear with toothed rail (MRGTR), and to improve the stability and safety of monorail transporters, this paper theoretically analyzed the MRGTR mechanism of toothed monorail transporters as well as established the MSEMT displacement model and its instantaneous velocity model. The vibration signals of MSEMT with four different parameters of toothed rail were collected by the acceleration sensor and signal acquisition system. The signals were analyzed by the Hilbert envelope demodulation method to investigate the influence of toothed rail parameters on meshing impact vibration. Moreover, taking the vibration acceleration amplitude of MSEMT and the vibration attenuation time of meshing impact as evaluation indexes, a test based on the three-factor and two-level orthogonal test was engaged with factors of toothed rail pressure angle, the ratio of L—the chord length of two adjacent roller centers of a roller gear—and rack pitch p (wheel-tooth ratio) and the load mass of the MSEMT. It showed that the impact of MRGTR was the main excitation source of the vibration of MSEMT. The pressure angle and wheel-tooth ratio both have a significant impact on the smooth operation of MSEMT, the latter to a greater extent. So did the interaction between wheel-tooth ratio and load mass. The amplitude of the characteristic frequency of the MSEMT decreased with the growth of the pressure angle. When the wheel-tooth ratio was cosα, the number of the characteristic frequency was less than that when it was 1, and the amplitude became smaller too. When the pressure angle was 15, the amplitude of vibration acceleration characteristic frequency decreased as a consequence of load mass increasing. At the pressure angle of 25, the amplitude of characteristic frequency decreased with the increase of load mass if the wheel-tooth ratio was 1, and the opposite result occurs in the case when the wheel-tooth ratio was cosα. This paper provides a theoretical basis and reference for improving the impact vibration of MRGTR and optimizing the design of the toothed rail.