Provided are a diffraction-based metrology apparatus having high measurement sensitivity, a diffraction-based metrology method capable of accurately performing measurement on a semiconductor device, and a method of manufacturing a semiconductor device using the metrology method. The diffraction-based metrology apparatus includes a light source that outputs a light beam, a stage on which an object is placed, a reflective optical element that irradiates the light beam onto the object through reflection, such that the light beam is incident on the object at an inclination angle, the inclination angle being an acute angle, a detector that detects a diffracted light beam that is based on the light beam reflected and diffracted by the object and a processor that measures a 3D pupil matrix for the diffracted light beam and analyze the object based on the 3D pupil matrix.