Dynamic decoupling (DD) can suppress decoherence caused by environmental noise, while in hybrid system it also hinders coherent manipulation between qubits. We realized the universal high-fidelity quantum gate set and the preparation of Bell states using dynamical decoupling gates (DD gates) in a silicon-based phosphorus-doped (Si:P) system, effectively resolving the contradiction between decoherence protection and manipulation of qubits. The simulation results show that the fidelity of the universal quantum gate set are all above 99%, and the fidelity of Bell state preparation is over 96%. This work realized the compatibility between coherent protection and high-fidelity manipulation of quantum states, provided a reliable theoretical support for high-fidelity quantum computing.