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A theoretic model is presented to take into account the roughness effects on phonon transport in Si nanowires (NWs). Based on the roughness model, an indirect Monte Carlo (MC) simulation is carried out to predict the lattice thermal conductivities of the NWs with different surface qualities. Through fitting the experimental data with the MC predictions, the scattering strength on phonons from the boundary, umklapp phonon–phonon processes and impurities can be estimated. It is found that the scattering on phonons by the roughness cell boundaries in a rough nanowire can reduce the phonon mean free path to be smaller than the nanowire diameter, the Casimir limit of the phonon mean free path in a flat nanowire for phonons engaged in completely diffused boundary scattering processes.