Identifying parameters in the system Hamiltonian is a vitally important task in the development of quantum technology. This paper investigates the problem of Hamiltonian identification for closed quantum systems and develops a new algorithm to achieve the task of identifying the Hamiltonian. Under the framework of standard quantum process tomography and without prior assumptions, we first convert the problem of Hamiltonian identification into an optimization problem and then design an iterative algorithm to numerically solve this problem. Numerical results for a two-qubit system are presented to show the effectiveness of the proposed algorithm through analyzing the mean squared error.