The running biomechanics of running shoes have been extensively investigated. However, there is limited knowledge about the use of bionic shoes compared to neutral shoes, along with the velocities involved in their use. The aim of this study was to examine the biomechanical alterations associated with various running velocities of bionic shoes. By removing different thicknesses of the forefoot section, bionic shoes created a more natural shape—close to that of a human foot. The study included 16 heel strike runners running at 10 km/h, 12 km/h and 14 km/h in bionic shoes and neutral shoes, respectively. A two-way ANOVA and SPM1d were employed for examining kinematic and kinetic differences. Regarding the results for the shoes, increased ROM was observed for the bionic shoes for the hip (p < 0.001) and ankle joints (p < 0.001). Ankle positive work (p < 0.001) and negative work (p = 0.042) also showed significant differences. Regarding the velocity results, hip ROM (p < 0.001) increased and peak knee angular velocity (p = 0.018) increased, while knee ROM (p = 0.023) decreased. The interaction effects only existed in hip (p = 0.031) and ankle (p = 0.008) ROM. The results of this study suggested that the impact of running propulsion in the bionic shoes was minimal. However, with increased velocities, the bionic shoes demonstrated the ability to absorb more force, created a more stable training environment, and contributed to injury prevention for the hip and ankle joints.