Purpose This study aims to investigate the prevalence of shock boundary layer interaction (SBLI) in air-breathing intake system is highly undesirable since this leads to high pressure gradients, typical stream mutilation and pressure drop. A novel flow control mechanism is incorporated in this research holding an array configuration of passive flow control device (micro ramps [MR]) that is adapted to improve the boundary layer stability. Design/methodology/approach Two geometric variants of the MR, namely, MR40 and MR80 is considered which reduce the pressure drop during SBLI. The incidence oblique shock wave angle of 34 degrees is considered for the modelling. Large eddy simulation (LES) turbulence model was used with subgrid models of Wall modelled LES, Smagorinsky-Lilly to compute the unsteady effects of SBLI control using micro vortex generators. The unsteady results are compared with steady Reynold's average Naviers-Stoke's equation for calibrating the turbulence models. Findings The array configuration of MR80 reduces the pressure drop by 22% as compared with no ramp configuration and also reduces the flow distortion in hypersonic inlet. The most affected region of the MR is in the vicinity of center-line. Quantitative results prove that the upstream influence of the shock waves has been largely reduces by MR80 array configuration as compared to single MR80 pattern configuration. Different vortex structures found in the experiments was exclusively predicted using LES. Originality/value This paper substantiates the requirement of MR array configuration for transferring the momentum from free stream to the boundary layer and thereby energizing the boundary layer. This process of energization delays the flow separation in hypersonic flow.