A near eye display system including a display screen, a graphic processing unit, a lens group, a focal length adjustment device, an interpupillary distance adjustment device, a detection unit, and a control unit is provided. Positions of a left-eye image and a right-eye image to be displayed on the display screen may be adjusted based on lateral displacement amounts of a left-eye lens and a right-eye lens, such that centers of the left-eye image and the right-eye image are respectively aligned with centers of the left-eye lens and the right-eye lens. Sizes (magnification) of the left-eye image and the right-eye image to be displayed on the display screen may be adjusted based on longitudinal displacement amounts of the left-eye lens and the right-eye lens, such that sizes of a visual left-eye image and a visual right-eye image seen by a user are identical. Operation methods thereof are also provided.