An exposure apparatus capable of preventing a reduction in its accuracy due to, for example, the influence of aging or the influence of heat is disclosed. Also disclosed is a method of controlling the same, and an alignment method for exposure. In one aspect, the exposure apparatus includes a main stage for adjusting a position of a substrate, a beam irradiation unit for irradiating a beam onto a mask, and a beam monitoring unit having a position fixed with respect to the main stage, and for recognizing the beam emitted from the beam irradiation unit and passed through one pattern of the mask.