The invention relates to a system for automatic dual-grating alignment in proximity nanometer lithography, comprising a light path part, an image processing part and a circuit control part, wherein the light path part comprises a laser source, a lens group, a mask, a silicon wafer, a mask grating, a silicon wafer grating, a beam splitter, an objective lens and a CCD (charge coupled device) image detector; lasers pass through the lens group and then forms uniform and collimated parallel lights which are subjected to diffraction for a plurality of times through the silicon wafer grating and the mask grating, and the two gratings have approaching periods and are superposed with a certain gap; certain two same-level diffraction light beams from the two gratings are subjected to interference superposition, Moire interference fringes with the period of being amplified compared with that of the original grating are formed on the surface of the silicon wafer grating, and then the Moire interference fringes are imaged on the CCD image detector by virtue of the objective lens. By processing images, phase difference of two groups of Moire interference fringes can be extracted, further the relative displacement of the mask and the silicon wafer can be calculated, and the silicon wafer is controlled to move by the circuit control part so as to realize complete alignment of the silicon wafer and the mask. By utilizing the system provided by the invention, real-time alignment can be achieved, the accuracy is high, and the automation of alignment can be realized.