Improving the control of heat flow at the nanoscale is essential for promoting its applications in many fields, such as energy conversion, thermal informatics, and communication technologies. Here we perform a systematic study on the synergistic effect of screw dislocations and surface resonators on thermal transport of Si nanowires and the corresponding mechanisms based on molecular dynamics simulations. We uncover that screw dislocations reduce the thermal conductivity by enhancing the anharmonicity of nanowires due to the nonhomogeneous stress field. For resonant structures, we demonstrate that the suppression of relaxation time is the main mechanism for thermal conductivity reduction. The suppression of relaxation time by more than two orders of magnitude below 4 THz dramatically reduces the resonant structure thermal conductivity, while the previously proposed group velocity reduction mechanism can only impede phonon transport beyond 4 THz slightly. By comparing the mechanisms produced by dislocations and resonators, we find that the resonators have a stronger effect over screw dislocations in impeding the phonon transport at low frequencies while it becomes opposite at high frequencies. As a result, they can be combined together to manipulate phonon transport synergistically at all frequencies. Our findings not only provide insights into the mechanisms of thermal conductivity engineering by screw dislocations and surface resonators, but they also illustrate a paradigm for ultralow thermal conductivity design through the tailoring of the entire frequency range of phonon transport.