Provided are three-dimensional (3D) data processing apparatus and method. 3D stereoscopic image common format data preserving common 3D image information is defined by converting 3D stereoscopic image data of each format to apply the same 3D image processing algorithm to 3D data of various formats, and native format data of each format is maintained to maintain merits of each format, and a format-specific algorithm table is maintained with respect to a common 3D image processing function, whereby the same 3D image processing algorithm may be applied to various 3D data and a unique algorithm allowing for maintaining the merits of each 3D data may be applied.