Abstract: In this paper, weak moving target detection in sea clutter is mainly studied. A novel adaptive fractional Fourier transform (FRFT) based algorithm is proposed for moving target detection in sea clutter, which combines LMS algorithm and FRFT method. At first, detection model of moving target with time-varying amplitude is established and the optimal transform angle is determined by calculating kurtosis of amplitude in FRFT domain. Grading iterative method is used for good accuracy of parameter estimation and fast calculation speed. Then, adaptive FRFT domain line enhancer (ALE) is employed to suppress sea clutter and improve signal to clutter ratio (SCR). Leakage factor is introduced into the update equation of weight vector to reduce memory effects on ALE and step size is normalized by the power of input signal with fast convergence. Target can be declared if the output signal is higher than the threshold and then parameters of moving target are estimated. In the end, X-band real sea clutter of IPIX radar is used for verification and the results present that the proposed algorithm has good convergence property and small mean square error (MSE). Weak moving target can be detected in low SCR (SCR=-5dB) environment with high detection probability (Pd=0.9), which indicates the effectiveness and robustness of the algorithm.