By applying first-principles Peierls-Boltzmann transport calculations, the lattice thermal conductivities of type-I, type-II, and type-VIII silicon clathrates are investigated. The lattice thermal conductivity, spectral lattice thermal conductivity, and lattice thermal conductivity versus mean-free path (MFP) of phonons, relaxation times, and the anharmonicity of selected Si clathrates are calculated and compared. The microscopic origin of the slight difference in the lattice thermal conductivity of Si-I/II/VIII clathrates is discussed extensively. Our calculations uncover that the impact of phonon group velocity on the lattice thermal conductivity is far from enough to explain the discrepancies in $ąppa$lat of studied Si clathrates and it mainly is a consequence of the shorter lifetimes of the acoustic modes in type-VIII structure. Similarity between phase space for three-phonon anharmonic scattering processes of studied silicon clathrates highlights the influence of three-phonon coupling strength and the further calculation of the frequency-resolved final state spectra re-emphasizes that the subtle differences arise from the stronger three-phonon interaction coefficients.