This paper presents a comprehensive study on the design and optimization of high-fidelity quantum gates for a two-qubit system formed by the electron and nuclear spins of a nitrogen-vacancy (NV) center in diamond. The authors use gate set tomography (GST) to systematically optimize the gates and achieve single-qubit gate fidelities of up to 99.999(1)%, and a two-qubit gate fidelity of 99.93(5)%. The gates are designed to decouple unwanted interactions between the qubits and the environment, and the results demonstrate significant improvements over previous methods. The high fidelities achieved provide a promising foundation for larger-scale quantum processing with color-center qubits. The study also includes detailed analyses of gate errors, context-specific single-qubit gates, and the implementation of an electron-nitrogen SWAP gate, which is used to store quantum states in the nitrogen quantum memory for over 100 seconds.This paper presents a comprehensive study on the design and optimization of high-fidelity quantum gates for a two-qubit system formed by the electron and nuclear spins of a nitrogen-vacancy (NV) center in diamond. The authors use gate set tomography (GST) to systematically optimize the gates and achieve single-qubit gate fidelities of up to 99.999(1)%, and a two-qubit gate fidelity of 99.93(5)%. The gates are designed to decouple unwanted interactions between the qubits and the environment, and the results demonstrate significant improvements over previous methods. The high fidelities achieved provide a promising foundation for larger-scale quantum processing with color-center qubits. The study also includes detailed analyses of gate errors, context-specific single-qubit gates, and the implementation of an electron-nitrogen SWAP gate, which is used to store quantum states in the nitrogen quantum memory for over 100 seconds.