Machined surface roughness has significant effects on the performance of micro-nozzles, which are fabricated by micro-machining. Machining process parameters greatly affect surface roughness, for that the manufacturers need to obtain optimal operating parameters. In this paper, machining parameters are optimized for micro-machining nozzle based on the characteristics of surface roughness. First, roughness model of nozzle milling with ball-end mill is presented. A case of nozzle surface is then given to verify the reliability of the roughness model proposed. Second, influences of surface roughness on nozzle average outlet velocity and thrust efficiency are investigated through computational fluid dynamics (CFD) analysis. It is found that vortical flow generates gradually with increasing of surface roughness, which leads to wasted energy increasing. When roughness value reaches a certain threshold, vortical flow is formed, which significantly reduces nozzle performances of velocity and thrust efficiency. Finally, micro-orthogonal machining experiments are performed. It is shown that the remarkable factor influencing the surface roughness of micro-nozzle is axial depth of cut.