In this paper, a novel flow perturbation model meant to investigate the effects of incoming wind shear on a hypersonic inlet/isolator is presented. This research focuses on the transient shock/boundary layer interaction and shock train flow evolution in a hypersonic inlet/isolator with an on-design Mach number of 6.0 under incoming wind shear at high altitudes, precisely at an altitude of 30 km with a magnitude speed of 80 m/s. Despite the low intensity of wind shear at high altitudes, the results reveal that wind shear significantly disrupts the inlet/isolator flowfield, affecting the shock wave/boundary layer interaction in the unthrottled state, which drives the separation bubble at the throat to move downstream and then upstream. Moreover, the flowfield behaves as a hysteresis phenomenon under the effect of wind shear, and the total pressure recovery coefficients at the throat and exit of the inlet/isolator increase by approximately 10% to 12%. Furthermore, this research focuses on investigating the impact of wind shear on the behavior of the shock train. Once the inlet/isolator is in a throttled state, wind shear severely impacts the motion of the shock train. When the downstream backpressure is 135 times the incoming pressure (p0), the shock train first moves upstream and gradually couples with a cowl shock wave/boundary layer interaction, resulting in a more significant separation at the throat, and then moves downstream and decouples from the separation bubble at the throat. However, if the downstream backpressure increases to 140 p0, the shock train enlarges the separation bubble, forcing the inlet/isolator to fall into the unstart state, and it cannot be restarted. These findings emphasize the need to consider wind shear effects in the design and operation of hypersonic inlet/isolator.