Using the atomistic nonequilibrium Green’s function, we find that thermal conductance of carbon nanotubes with presence of topological lattice imperfects is remarkably reduced, due to the strong Rayleigh scattering of high-frequency phonons. Phonon transmission across multiple defects behaves as a cascade scattering based with the random phase approximation. We elucidate that phonon scattering by structural defects is related to the spatial fluctuations of local vibrational density of states (LVDOS). An effective method of tuning thermal transport in low-dimensional systems through the modulation of LVDOS has been proposed. Our findings provide insights into experimentally controlling thermal transport in nanoscale devices.