Transient interference can dramatically degrade the performance of over-the-horizon radar (OTHR). A novel transient interference suppression method based on structured low-rank matrix decomposition is proposed in this paper. Unlike most of the traditional interference suppression methods which need three steps: detect interferences, excise corrupted data and reconstruct excised data, the proposed method formulates the interference suppression as a Hankel matrix decomposition problem and suppress the interference via a single process of optimization. In addition, the proposed algorithm can suppress not only the interferences including the weak and strong ones, but also the noise. Simulation and experimental results have demonstrated the effectiveness of the proposed method.