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For the problem of time-delay estimation for sub-sampling sinusoidal signals, the paper proposes a novel method composed of multi-period sampling and multi-layer correlation. This method can reduce the complexity of estimation and improve the range of time-delay estimation and its stability. It also has an excellent performance to reduce the effect of noise and interference. The important contribution of this new method is that it adapts to high frequency (HF) signal processing, such as in radar, electronic warfare (EW), etc. It accelerates the digital receiver realization of an HF system. Simulations show the performance and obvious advantage of the new method.