A multiple-relaxation-time lattice Boltzmann model of Couette flow is developed to investigate the rarified gas flow through microchannels with roughness characterized by fractal geometry, especially to elucidate the coupled effects of roughness and rarefaction on microscale gas flow in the transition flow regime. The results indicate that the surface roughness effect on gas flow behavior becomes more significant in rarefied gas flow with the increase of Knudsen number. We find the gas flow behavior in the transition flow regime is more sensitive to roughness height than that in the slip flow regime. In particular, the influence of fractal dimension on rarefied gas flow behavior is less significant than roughness height.