This invention is directed to a document processing system and control method thereof. The system stores a plurality of items of document data each containing metadata pertaining to the contents of each item of document data, and relation information representing the relations between the plurality of items of document data. When scanned image data or facsimile-received image data is input, document data related to the input image data is specified among the plurality of items of stored document data, based on the metadata contained in each item of document data. Relation information representing the relation between the input image data and the specified related document data is stored. Even document data obtained from a paper document is able to be stored as document data subjected to search processing.