Abstract: Existing methods for suppressing transient interference suffer from high computation cost due to that most of them rely on clutter suppression. To solve this problem, a novel method based on Complex Empirical Mode Decomposition (CEMD) is proposed to suppress transient interference in Over-The-Horizon Radar (OTHR). After decomposed radar echoes by using CEMD it accomplishes the detection of transient interference, excision of transient interference, and data reconstruction at the same time. The proposed method does neither require to perform clutter suppression, nor to reconstruct data by using prediction algorithm of AutoRegressive (AR) model. Thus, this method is of low complexity and high feasibility. Processing of the real data from OTHR system shows that the algorithm can efficiently suppress transient interferences.