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Nonadiabatic holonomic quantum computation~(NHQC) provides an essential way to construct robust and high-fidelity quantum gates due to its geometric features. However, NHQC is more sensitive to the decay and dephasing errors than conventional dynamical gate since it requires an ancillary intermediate state. Here, we utilize the Hamiltonian reverse engineering technique to study the influence of the intermediate state-decoherence on the NHQC gate fidelity, and propose the novel schemes to construct the arbitrary single-qubit holonomic gate and nontrivial two-qubit holonomic gate with high fidelity and robustness to the decoherence. Although the proposed method is generic and can be applied to many experimental platforms, such as superconducting qubits, trapped ions, quantum dots, here we take nitrogen-vacancy (NV) center as an example to show that the gate fidelity can be significantly enhanced from 89\% to 99.6\% in contrast to the recent experimental NHQC schemes [Phys. Rev. Lett. 119, 140503 (2017); Nat. Photonics 11, 309 (2017); Opt. Lett. 43, 2380 (2018)], and the robustness against the decoherence can also be significantly improved. All in all, our scheme provides a promising way for fault-tolerant geometric quantum computation.