The present invention relates to an apparatus and method for generating a three-dimensional image of a polymer substance. The three-dimensional image generating apparatus of the present invention comprises: a specimen state adjustor for adjusting a temperature or pressure of a solid specimen in order to maintain, in a solid state, the solid specimen including a plurality of polymer substances; an image collector for collecting a partial image of the plurality of polymer substances exposed on a surface of the solid specimen; a low molecule image database for storing an image of an element low molecule substance; and an image processor for generating a three-dimensional image of the polymer substance by matching the collected partial image with an image in the low molecule image database.