Abstract A new moving target detection algorithm is proposed based on the joint fractal properties discriminant of sea clutter in FRactional Fourier Transform (FRFT) domain. At first, statistical characteristic of sea clutter data in FRFT domain is analyzed and simulations of fractal curves in different polarizations are conducted, which indicates the self-similarity feature. Then, determination method of fractal parameters and scale-invariant interval is given and influence of transform order on the estimation of fractal parameters is also discussed. Finally, differences of fractal dimension and intercept in FRFT domain, which are calculated from adjacent range bin or time series of radar echo, can be used as test statistic. Real sea clutter in different polarizations is used for verification and the results present that the proposed algorithm has good performance for weak moving target detection and can also give high estimation accuracy of moving conditions.