Based on the Direct Simulation Monte Carlo (DSMC) method, an unsteady flow, which is caused by the interaction of two counter-flow jets with a hypersonic free stream, is constructed and simulated in the rarefied regime for the flight altitude of 90 km. In this complex three-dimensional rarefied flow, although the hypersonic free stream and all counter-flow jets are stable, their interaction area has great instability. This signifies that this extensive interaction area will not reach a final stable state in the DSMC simulation process. This study exhibits the unsteady evolution of the interaction area.