The spreading of hydrogen jet within the combustion chamber is extremely important for the fuel consumption and enactment of scramjet engines. In this article, a numerical method is used to simulate the influence of wavy wall on distribution of the hydrogen cross flow jet in the downstream of the injectors. To examine the main role of wavy surface on the fuel distribution, a 3-D model is selected with an appropriate grid to detect the primary interaction of the hydrogen fuel jet with the deflected supersonic free stream. Code was developed to solve the Navier-stokes equation with energy and species mass transport equations. This study compares the effect of the amplitude of the wavy upstream wall on the main flow structure and hydrogen fuel distribution within the confined channel. The effects of hydrogen jet pressure on the main stream are also studied. Our findings display that the mixing rate of fuel inside the combustor rises about 35% when high amplitude surface wall is applied in the upstream of jet.