We investigated the thermal transport properties of magnetic van der Waals materials, TMPS3 (TM = Mn, Ni, and Fe), using the time-domain thermoreflectance technique. We determined the cross-plane thermal conductivity, which turns out to be relatively low, i.e., about 1W m(-1) K-1 for all TMPS3 investigated. When compared with previous results of graphite and transition metal dichalcogenides (TMDs), thermal conductivity becomes smaller as it goes from graphite to TMDs to TMPS3, and the difference is larger at low temperature, e.g., around 50K. From the Callaway model analysis, we could attribute the large thermal conductivity reduction for TMPS3, particularly at low temperature, to the phonon scattering from the boundary. We actually confirmed the existence of the large population of the stacking faults with the cross-sectional transmission electron microscopy image of MnPS3. This suggests that intrinsic or extrinsic stacking faults formed in van der Waals materials and their heterostructures can play an important role in reducing the cross-plane thermal conductivity as a source of the boundary scattering.