Implicitly implemented large eddy simulation (LES) with a fifth-order WENO scheme was conducted in this study. Based on Navier-Stokes equations, this LES was carried out to explore the origin of momentum deficit caused by a supersonic micro-ramp at flow conditions of $M_a$ = 2.5 and $Re_{ heta}$ = 5760. The numerical results were validated through qualitative and quantitative comparisons with existing experimental data. After describing the aerodynamic properties of the supersonic wake, such as the deficit and the streamwise vortices, the momentum deficit was later detected to originate from the lower portion of the upstream boundary layer, while the high momentum fluid originated from close to the wall at the upper portion. Position alternation trigged by the micro-ramp was finally proposed as a revised mechanism.