Abstract: Counter-flow engines are often used for aircraft slowing or separating. In order to study the interaction between the counter-flow jets and free stream at high altitudes, the rarefied flow driven by two counter-flow jets and hypersonic free stream was constructed. By the direct simulation Monte Carlo (DSMC) method, it is found that a large area of mutual interference will be formed under the condition of rarefied free stream, and there are serious unsteady flow phenomena in the interference area. According to preliminary analysis, the range and unsteady evolution of the interference area are closely related to the kinetic energy of free stream and the flow rate of counter-flow jets.