The gear is one of the important parts of a rotary gearbox. Once catastrophic gear failure occurs, it will cause a great threat to production and life safety. The crack is an important failure factor causing changes in time-varying stiffness and vibration response. It is difficult to effectively identify the vibration response and meshing stiffness changes when there is a fine crack in the gear. Therefore, it is of great importance to improve the accuracy of meshing stiffness calculation and dynamic simulations under micro-cracks. Investigations of meshing stiffness and the vibration response of a gearbox is almost all about fixed gear shape parameters. However, the actual production process of gear system needs to change gear shape parameters. In this paper, the meshing stiffness and vibration response of the dynamic simulation signals of gear teeth with different crack depths at different tooth shape parameters (the pressure angle, the modulus, and the tooth number) were calculated, respectively. The influence of cracks on the vibration response was investigated by the fault detection indicators, the Root Mean Square (RMS), the kurtosis, and the crest factor. The result shows that when the pressure angle and modulus change, the vibration response changes erratically. However, when the tooth numbers change, the vibration response changes regularly. The results could be a guide for choosing gears in different shape parameters when system stability is the aim.