The boundary layer transition of sonic nozzle is affected by many factors, including Reynolds number, macro structure (throat diameter), meso-micro surface structure (wall roughness, waviness), turbulence intensity, wall heat transfer and so on. Therefore, in order to analyse the influences of macrostructure, meso-micro surface structure and turbulence intensity on boundary layer transition, the Cd and geometric dimension (throat diameter, d, average roughness, Ra, maximum roughness, Rz, and waviness, wa) of sonic nozzles with throat diameter of 1.919 mm, 3.808mm, and 7.453 mm were experimental investigated and measured. Furthermore, a series of CFD simulations through the transition SST model for axisymmetric nozzles were established to research the variation law of boundary layer transition and Cd of the sonic nozzle when Reynolds numbers ranges from 4.6×10 4 to 4.7×10 7 and different turbulence intensity (Tu) and meso-micro surface structure (Ra, Rz and wa). The validity of the simulation model was confirmed by the experimental data of National Institute of Metrology of China (NIM). Finally, the relationships between the boundary layer transition and Tu, Ra, Rz and wa were obtained.