The present invention provides a sensor alignment method using in a scanning apparatus. Firstly, providing a housing on the transparent board and defining a alignment area below the housing, the sensor locates under the alignment area and the light source locates aside the alignment area; then, moving the sensor out of underside of the alignment area and measuring intensity of light source to obtain a regional position where the brightest position on the transparent board, and moving the sensor to underside of the regional position; and finally, moving the sensor and the light source into the alignment area, and synchronously moving the sensor and the light source out to capture images. This invention prevents the tolerance formed in the printing process and the alignment point determination of the sensor is more precise, and furthermore, the scanning area is increased and the manufacturing cost is reduced.