Provided are a method and system for generating an input file using meta representation of compression of graphics data, and an animation framework extensions (AFX) encoding method and apparatus. The method of generating an input file includes preparing an extensible MPEG-4 textual (XMT) schema that defines a compression node, encoding parameters, and BitWrapperEncodingHints; preparing an XMT2BIFS style sheet that supports conversion of an input XMT file into a scene file according to the XMT schema, and an XMT2MUX style sheet that supports conversion of the input XMT file into a mux file according to the XMT schema; generating the scene file and the mux file by parsing the input XMT file according to the XMT schema using the XMT2BIFS and XMT2MUX style sheets; determining whether the scene file contains uncompressed graphics data; and compressing the graphics data into a bitstream using the encoding parameters and generating a modified scene file and a modified mux file, when uncompressed graphics data is present in the scene file. Accordingly, it is possible to allow an author to easily express or compress three-dimensional (3D) graphics data using meta representation during authoring of 3D contents and generate an input file that can be input to an MPEG-4 encoder. Therefore, it is possible to visualize 3D graphics data or animation data in real time even at a low network bandwidth.