A network-based document protection system for the protection of business secret includes: a template module configured to search for the template information of a template stored in a template database (DB) or the document information of a document stored in a document DB, and to execute the corresponding template or document via a dedicated application; an authentication module configured to generate the document information by including the identification code of an operator in the corresponding template information or to identify a corresponding operator by recognizing an identification code from the document information of the executed document, according to the execution procedure of the template module; and a security module configured to store the document, generated or updated via the dedicated application, in the document DB, and to perform security processing on the document.