Provided is a parallelism measuring system and a method thereof, wherein the system includes a measured module, which includes a measured unit; a reference unit; and an optical measuring unit including an optical measuring module and a shift module. A lower surface of the measured unit is a measured surface and an upper surface of the reference is a reference surface. The optical measuring module includes a light source unit, a reflecting unit, and a sensing unit. A collimated beam is emitted from the light source unit and sequentially reflected by the measured surface, the reflecting unit and the reference surface to the sensing unit. The sensing unit senses location of the collimated beam and thereby calculates interval distance between the measured surface and the reference surface. By using the shift module to move the optical measuring module, the interval distance between different points may be measured.