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Multiple maneuvering targets signal processing in high frequency radar is challenging due to the following difficulties: the interference between signals is severe because of significant spread of the target Doppler spectrum, the low signal to clutter ratio (SCR) environment degrades the performance of signal processing algorithms. This paper addresses this challenging problem by using an S2-method and an adaptive clutter rejection scheme. The proposed S2-method improves the S-method by eliminating interference between signals, and thus it enables multi-target signals to be reconstructed individually. The proposed adaptive clutter rejection scheme is based on an adaptive notch filter, which is designed according to the envelop of the clutter spectrum. Experiments with simulated targets added into radar sea clutter echo and real air target data illustrate the effectiveness of the proposed method.