In this article, numerical simulations were done to study the influence of the various hydrogen injections on the mixing rate in the cavity flameholder of the scramjet. This study tried to present the main effective parameters on the flow feature and distribution of the hydrogen jet within a cavity in supersonic free stream domain. In order to simulate the cavity flameholder with micro air/fuel jets, a three-dimensional model is chosen and computational fluid dynamic approach is used for the simulations. The effect of significant parameters is studied by using the Reynolds-averaged Navier-Stokes equations with Menter's Shear Stress Transport (SST) turbulence model. The effect of horizontal and vertical fuel injection is comprehensively studied. Moreover, the characteristics of the mixing in various free stream velocities (M = 1.2, 2.2 and 3.2) are examined and the effects of micro air jet on the size of ignition domain for preserving flame holder are investigated. Results show that the increase of free stream Mach number significantly enhances the mixing of horizontal fuel injection in the cavity. The obtained results reveal that the injection of micro air jets enhances the mixing rate in low Mach number (M = 1.2). Our findings also show that vertical hydrogen injection considerably increases the mixing zone within the cavity and the mixing rate significantly improves by rising free stream velocity. (C) 2018 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.