To solve the problem of low efficiency of NOx emission reduction in self-reflux burners, this study is based on the concept of coordinated control of self-reflux burner structural and thermal parameters. After completing the structural design and optimization of thermal parameters, we continue to adjust the two key structural parameters: the nozzle axis distance and the length of the cylindrical section, to minimize NOx emissions. These are the two parameters that chiefly affect the mixing of flue gas and fuel gas. The results show that increasing nozzle axis distance can delay the mixing of gas and air and create a more uniform oxygen concentration field for the combustion process. The maximum combustion temperature is reduced from 1973.65 K to 1935.88 K and the volume fraction of NOx in the flue gas is reduced from 188.08×10−6 to 143.47×10−6. However, compared with the nozzle axis distance, the length of the cylindrical section of the burner has little effect on the mixing of the flow field. Under different cylindrical section lengths, the maximum combustion temperature does not change more than 3 K, and the volume fraction of NOx in the flue gas changes within 5×10−6.