Recently, the magnitude of electronic data interchange (EDI) document processing for the handling of port logistics is abruptly being increased. The existing system processes EDI documents in a script mode, but due to a complicated script preparation procedure and low document processing efficiency, it cannot meet the demand as the usage flow of documents increases. In this paper, an EDI electronic document processing system was designed and implemented in a document scanner and mapper, which are binary form electronic document processing tools and do not require script files during the conversion of extensible markup language (XML)-based electronic documents. This new system has the merits of XML features during reading and writing with improved speed, usage convenience, and good portability on systems when compared to the conventional ones.