The interaction between hypersonic free stream and side jet flow at high altitudes is investigated by using the direct simulation Monte Carlo (DSMC) method. In order to alleviate the difficulty associated with the large density difference between the free stream and the side jet flow and to simulate the two flows simultaneously, a weighting factor technique is applied. For validation, the corner flow over a pair of plates perpendicularly attached is calculated with and without a side jet, and the results are compared with experiment. For a more realistic configuration, the flow past a blunted cone cylinder shape is solved. The leeward or windward jet is injected into the free stream and the effect on the aerodynamic force and moment is observed at various flow angles. The lambda shock effect and the wake structure are studied in terms of the surface pressure differential. A higher interaction between the free stream and the side jet flow is observed when the side jet is injected in the windward direction.