Molybdenum disulfide (MoS2) has attracted significant attention due to its good charge carrier mobility, high on/off ratio in field-effect transistors and novel layer-dependent band structure, with potential applications in modern electronic, photovoltaic and valleytronic devices. Despite these advantages, its thermal transport property has often been neglected until recently. In this work, we probe phonon transport in few-layer MoS2 flakes with various point defect concentrations enabled by helium ion (He+) irradiation. For the first time, we experimentally show that Mo-vacancies greatly impede phonon transport compared to S-vacancies, resulting in a larger reduction of thermal conductivity. Furthermore, Raman characterization shows that the in-plane Raman-sensitive peak E2g1 was red-shifted with increasing defect concentration, corresponding to the gradual damage of the in-plane crystalline networks and the gradual reduction in the measured thermal conductivity. Our work provides a practical approach for atomic-level engineering of phonon transport in two-dimensional (2D) layered materials by selectively removing elements, thus holding potential applications in designing thermal devices based on various emerging 2D materials.