We study the mixing of rarefied gases in a T-shape micromixer by means of fully three-dimensional Monte-Carlo direct simulations. In contrast to previous 2D-results, the characteristics of the channel walls (thermal or specular) have significant effect on the mixing efficiency. For the 3D case, we characterize the mixing efficiency in dependence on temperature and mass density of the gases. Based on kinetic theory arguments, we develop a theoretical model in good agreement with the simulation results. In particular, the theoretical prediction of system size scaling agrees well with the simulation.