Abstract-Quantum Hamiltonian identification is important for characterizing the dynamics of quantum systems, calibrating quantum devices and achieving precise quantum control. In this paper, an effective two-step optimization (TSO) quantum Hamiltonian identification algorithm is developed within the framework of quantum process tomography. In the identification method, different probe states are inputted into quantum systems and the output states are estimated using the quantum state tomography protocol via linear regression estimation. The time-independent system Hamiltonian is reconstructed based on the experimental data for the output states Index Terms-Quantum system, Hamiltonian identification, process tomography, computational complexity.