A reference linking service that is connection of each other different information resource need to setup the reference database and to match identifier. CrossRef, PubMed and Web Of Science etc. the many overseas agencies developed reference linking service, that they used the automatic tools of Inera eXstyles, Parity Computings Reference Extractor etc. and setup in base DOI and PMID etc. Domestic the various agencies of KISTI(Korea Institute Science and Technology of Information), KRF(Korea Research Foundation) etc are construction reference database. But each research communities adopts a various reference bibliography writing format. As, the data base construction which is collect is confronting is many to being difficult. In this paper, We developed the Citation Matcher System. This system is automatic parsing the reference string to metadata and matching DOI, PMID and KOI as Identifier. It is improved the effectiveness of reference database setup.