To realize alignment of a mask and a wafer with high throughput and high accuracy.

The charged beam proximity lithography method comprises a step for imaging first marks put at two positions on a mask and second marks put at two positions on a wafer from orthogonal directions simultaneously by a first microscope imaging apparatus having two sets of image forming optical systems capable of focusing on one first and second marks and a second microscope imaging apparatus having two sets of image forming optical systems capable of focusing on the other first and second marks, a step for measuring positional shift based on the image signals of one first and second marks obtained from the first microscope imaging apparatus and measuring positional shift based on the image signals of the other first and second marks obtained from the second microscope imaging apparatus, a step for aligning the mask and wafer based on the measured positional shift, and a step for transferring a mask pattern to a resist layer on the wafer.