The mismatch between echo and replica caused by underwater moving target(UMT)s radial velocity degrades the detection performance of the matched filter(MF) for the linear frequency modulation(LFM) signal. By using the focusing property of fractional Fourier transform(FRFT) to that signal, a detection algorithm for UMTs LFM echo based on the discrete fractional Fourier transform(DFRFT) is proposed. This algorithm is less affected by the targets radial velocity compared with the other MF detection algorithm utilizing zero radial velocity replica(ZRVR), and the mathematical relation between the output peak positions of these two algorithms exists in the case of existence of target echo. The algorithm can also estimate the target distance by using this relation. The simulation and experiment show that this algorithms detection performance is better than or equivalent to that of the other MF algorithm utilizing ZRVR for the LFM echo of UMT with unknown radial velocity under reverberation noise background.