Identifying Hamiltonian of a quantum system is of vital importance for quantum information processing. In this Letter, we realized and benchmarked a quantum Hamiltonian identification algorithm recently proposed [Phys. Rev. Lett. 113, 080401 (2014)]. we realized the algorithm on liquid nuclear magnetic resonance quantum information processor using two different working media with different forms of Hamiltonian. Our experiment realized the quantum identification algorithm based on free induction decay signals. We also showed how to process data obtained in practical experiment. We studied the influence of decoherence by numerical simulations. Our experiments and simulations demonstrate that the algorithm is effective and robust. Introduction.-One critical task is to characterize a quantum system so that it can be used for quantum information processing tasks, such as quantum teleportation [1], quantum cryptography [2,3], quantum computation [4,5] and quantum metrology [6]. One way of fully characterizing a quantum system is doing quantum processing tomography (QPT). The QPT approach requires an exponential number of experiments, which makes it difficult to be realized for even a small sized quantum system [7][8][9][10].