Abstract: FLUENT 6.1 software was applied to simulate the supersonic flow in micro convergent-divergent nozzle.The simulation was complemented by computing steady two-dimensional Navier-Stokes(N-S) equations to study the effects of flow fields and performance of thruster from throat structure asymmetry.The asymmetry of throat was caused by deviation of throat upper vertex from lower vertex in x direction.The simulation results show that the asymmetry of throat causes fluids perturbation inside thruster,mass flow rate increases,and x direction thrust force decreases while additional y direction thrust force is produced at the exit of thruster.