Abstract:  On the basis of the detection and parameter estimation model of multiple moving targets, a new algorithm based on wavelet packet transform (WPT) and fractional Fourier transform (FRFT) is proposed for weak moving targets detection in sea clutter. The multi-resolution property of WPT and the characteristic of good energy concentration on LFM signal in FRFT domain are combined together. At first, optimal wavelet tree is calculated using “minimum Shannon entropy” and threshold censored method is used to suppress sea clutter of different frequency bands. Then, take the absolute amplitude of signal after FRFT as test statistic and search for peaks in two dimensions with the threshold. Grading iterative method is used for parameter estimation with fast calculation and the shading problem between multiple targets is solved through “CLEAN” method. In the end, IPIX real sea clutter data is used for verification and the results indicate that the proposed algorithm has a good performance of detecting multiple moving targets in low SCR conditions (about -10dB). It proves that the algorithm can improve operational speed and precision, and also be of better anticlutter interference capability.