The gas flow characteristics in rectangular cross section converging–diverging micronozzles incorporating the effect of three-dimensional (3D) rough surface topography are investigated. The fractal geometry is utilized to describe the multiscale self-affine roughness. A first-order slip model suitable for rough walls is adopted to characterize the slip velocities. The flow field in micronozzles is analyzed by solving 3D Navier–Stokes (N–S) equation. The results show that the dependence of mass flow rate on the pressure difference has a good agreement with the reported results. The presence of surface topography obviously perturbs the gas flow near the wall. Moreover, as the surface roughness height increases, this perturbation induces the supersonic “multiwaves” phenomenon in the divergent region, in which the Mach number fluctuates. In addition, the effect of 3D surface topography on performance is also investigated.