A positioning method in a microprocessing process of bulk silicon comprises the steps of: fabricating, on a first surface of a first substrate (10), a first pattern (100), a stepper photo-etching machine alignment mark (200) for positioning the first pattern, and a double-sided photo-etching machine first alignment mark (300) for positioning the stepper photo-etching machine alignment mark; fabricating, on a second surface, opposite to the first surface, of the first substrate, a double-sided photo-etching machine second alignment mark (400) corresponding to the double-sided photo-etching machine first alignment mark; bonding a second substrate (20) on the first surface of the first substrate; performing thinning on a first surface of the second substrate; fabricating, on the first surface of the second substrate, a double-sided photo-etching machine third alignment mark (500) corresponding to the double-sided photo-etching machine second alignment mark; and finding, on the first surface of the second substrate by using the double-sided photo-etching machine third alignment mark, a corresponding position of the stepper photo-etching machine alignment mark.