The utilization of supersonic nozzles to accelerate and cool the flow in the chemical oxygen-iodine laser is a significant progress in laser research. However, there are complex three-dimensional structures in the supersonic flow field. The relationships between flow structures and laser outputs are important criterions on the design of pneumatic components. The simulation system presented in the paper contains three blocks: the chemical flow calculation block, the optical calculation block and thermal structure calculation block. With the numerical platform, the analysis of the performance of laser under different flow conditions is carried out and the focus is the influence of the shock waves in the flow field on the near field laser output. According to the analysis, optimal methods are proposed. It makes an increase of the beam quality (F factor) of 45%.