An apparatus and method for segmenting a medical image are provided. The apparatus includes a user interface unit, which provides interface with a user, a volume data input unit, which inputs medical image information; a two-dimensional image display control unit, which receives the volume data, generates and displays a two-dimensional image corresponding to a predetermined position in the medical image, and performs segmentation of the two-dimensional image; and a three-dimensional image display control unit, which receives the volume data, generates and displays a three-dimensional image with respect to the medical image, performs segmentation of the three-dimensional image, transmits the result of the segmentation to the two-dimensional image display control unit, receives position information of the two-dimensional image and the result of the segmentation of the two-dimensional image form the two-dimensional image display control unit, and displaying them on the three-dimensional image.