A kind of nanometer lithography alignment method for two dimensional (2D) synchronization alignment in proximity lithography is presented. This method is based on the moiré effect. Two superposed 2D gratings with slightly different periods are adopted to generate a set of periodic moiré fringes, the period of which is hugely magnified with regard to that of two gratings and the relative displacement of gratings is encoded in the phase of fringes. Using the independent spectrum distribution of x and y direction in the Fourier spectrum and parsing the phase information on the transverse and longitudinal of moiré fringe by Fourier transformation can realize two dimensional high precision synchronization alignment. A kind of complex amplitude distribution model about two Ronchi 2D gratings alignment is built. Then, the relationship between the offsets of substrate and mask with moiré fringe is derived on the basic of this model. A simulation analysis about built model using computer is performed. The result shows that the accuracy can reach 2 nm when noise is considered; an experiment is made to test this alignment method after numerical computation. The accuracy of the result can reach 22 nm.