There are provided an image processing apparatus for registering medical images having different modalities and a method for controlling the same. A reference location is designated in advance, a pre-designated cross-sectional image of an object is used, a corresponding location is extracted, and then image registration is performed. The image processing apparatus according to an exemplary embodiment includes a communication unit configured to receive a first medical image and a second medical image having a different modality from the first medical image of an object from a first medical apparatus and a second medical apparatus, respectively; and an image processing unit configured to extract a pre-designated cross-sectional image from the second medical image, extract a location corresponding to a reference location of the object from the extracted cross-sectional image, and perform registration of the second medical image and the first medical image corresponding to the extracted cross-sectional image.