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When the rocket uses low-orbit satellite space-based measurement and control, due to the relatively large Doppler shift in relative motion, a spread spectrum system is needed to improve anti-interference; the spread spectrum signal under high dynamic conditions often uses partial matched filtering based on FFT (PMF-FFT) algorithm, but due to the introduction of FFT, this algorithm has serious scallop loss, which affects the system’s capture performance. Through the improved method of adding a Hamming window to the system, theoretical analysis and simulation show that it effectively suppresses scallops. Loss has a certain meaning for the acquisition of spread spectrum signals.