Abstract: ‍ ‍To achieve frequency tracking estimation of Frequency-Hopping （FH） signal， a multi-channel-based frequency estimation method of FH under-sampling signal is proposed. A frequency correction algorithm based on fast Fourier transform （FFT） and 3-spectral line equation is proposed to increase frequency estimation accuracy of short sequence signal by using China remainder theorem （CRT）. Compared with the existing two frequency correction algorithms based on discrete Fourier transform （DFT）， the number of zero padding for a sequence in the proposed algorithm is flexible. And an error detection mechanism is proposed to judge whether the frequency estimation is correct， and the reliability of the algorithm is improved. Simulation experiments demonstrate that the frequency estimation precision of the proposed algorithm is better than that of the existing algorithms. The proposed algorithm can improve estimation precision and signal-to-noise ratio （SNR） threshold， and reduce error floor by increasing the number of zero padding. And the accuracy of error detection is higher than 95.5% in the range of -23 dB to 8 dB SNR.