The laser transmission welding process is simulated based on the analysis of the real three-dimensional surface topography. The surface roughness of polycarbonate (PC) sample is measured by using a surface-roughness measuring instrument, the mathematical model of the surface roughness profile is built, and the solid modeling is done. The laser welding of smooth surfaces and real rough surfaces are simulated with the software of ANSYS Fluent, and the fracture morphology of the weld is analyzed. The results show that the welding strength of the rough PC surface is lower than that of the smooth surface.