A pattern inspection apparatus includes a transmitted illumination optical system to illuminate change the shape of a first inspection light, a reflected illumination optical system to illuminate a mask substrate with a second inspection light by using an objective lens and a polarizing element, and let a reflected light from the mask substrate pass therethrough, a drive mechanism to enable the polarizing element to be moved from/to outside/inside an optical path, a sensor to receive a transmitted light from the mask substrate illuminated with the first inspection light during stage moving, and an aperture stop, between the mask substrate and the sensor, to adjust a light flux diameter of the transmitted light so that the transmitted light reaching the sensor can be switched between high and low numerical aperture (NA) states with which the transmitted light from the mask substrate can enter the objective lens.