This paper presents a novel mechanism for self-organization of structure among documents based on process-oriented relations. Process-oriented relations represent operations and temporal distance between uses of documents in users' working processes. A complex network of process-oriented relations is rearranged as a multi-layered document network (MLDN) with a recursive hypergraph structure. The MLDN is self-organized by two kinds of autonomous agent: a document agent and a group agent. This facility provides up-to-date, easy-to-understand structure among documents, and helps users' understanding of relations between documents.