The effects of silicon (Si) doping on the in-plane and cross-plane thermal transport of suspended and silicon dioxide (SiO2) supported graphene were investigated via molecular dynamics simulations. Due to the large mismatch in atomic mass and interaction with neighboring carbon atoms, Si can act as an effective phonon scatterer, thus suppressing the thermal transport. In this study, we evaluated the contributions of mass and interaction mismatches of Si dopants to the reduction in the in-plane thermal conductivity and the cross-plane thermal resistance through systematic control of the dopant's properties. 2% Si doping reduces the in-plane transport of suspended graphene by ~94% due to the increased scattering, while the SiO2-supported graphene is less affected. The phonon scattering by Si linearly increases with the Si content, and the interaction mismatch has a greater influence on the phonon kinetics during in-plane transport than the mass mismatch. In contrast, the cross-plane transport is enhanced by Si doping, decreasing the interfacial thermal resistance by ~30%, because of the stronger interfacial interactions by weaker in-plane bonding and the smaller atomic mass mismatch with the substrate material. The enhanced understanding of doping effects on thermal transport from this research is expected to provide insights for effective thermal transport control in various graphene structures.