The fringe pattern analysis method based on the two-dimensional (2D) analytic wavelet transform (AWT) is proposed for the interference fringe pattern with multi-frequency that occurs in two grating marks in alignment of nanolithography. The multi-frequency of fringe is analysed by the multi-scale of the 2D wavelet transform (WT) first. The separation of the amplitude and phase is processed by the analytic wavelet basis function. The phase correlating to the offset is extracted through the 2D wavelet ridge method finally. The sign ambiguities which always occur in the process of analyzing closed fringe pattern are removed through the discontinuities of the angel in the 2D wavelet ridge. The feasibility of the method is verified by numerical simulation and experiment, and the comparisons of the traditional frequency-based phase analysis method are given. The results show that the noises brought by the fluctuation in the optical path in the fringes can be filtered effectively at the course of acquiring the phase information through the method with good adaptability.