Since 2007 Indonesian governments try to encourage every region to develop their regional innovation system (RIS) as a strategy to enhancing national innovation system (NIS). Lamongan is one of the regencies located on the north coast of East Java, it has long coastline along 47 km. Realize of potential Lamongan in their maritime sector, Ministry of Industry Indonesia and East Java Government has established the northern region of Lamongan Regency especially in Brondong sub-regency as a special economic region for maritime industry sector land with 200 hectares that will be developed soon. Therefore Lamongan Regency government agreed to develop their Regional Innovation System by using theme “Development of Sustainable Maritime Industry Based Mina-Agro-Tourism”. Leading sector of maritime industries in Lamongan is shipbuilding yard and fisheries. Bring the sustainable concept to shipbuilding industry can increase competitiveness of a shipyard and increase opportunity to reach new market. By using system dynamic approach this research aim to formulate linkage indicator for establishing the appropriate policy for development maritime industry with environmental sound in order to strengthen regional innovation system in Lamongan regency