Japan Aerospace Exploration Agency (JAXA) is investigating High Mach Integrated Control experiment (HIMICO) to realize a Mach 5 class hypersonic aircraft. Mass capture ratio (MCR) measured in the supersonic wind tunnel test is 15-40% lower than that analytically expected. This is caused by the spillage from the side-clearances between sidewalls and 2nd/3rd ramps. The CFD analysis of the model with the side-clearances agrees with the experiment result within 5% error. In this study, the side-clearance effect on the supersonic air-inlet performance is investigated by numerical simulation. With increasing the width of the side-clearance, the scale of the flow separation on the 2nd ramp gets larger. There are two types of flow separation, at center line and at the side wall. These two types of flow separation increases pressure at the entrance of the inlet and flow is pushed out. This causes MCR reduction.