In order to design optimal biomass utilization system for rural area, OMNIBUS (The Optimization Model for Neo-Integrated Biomass Utilization System) has been developed. OMNIBUS can derive the optimal system configuration to meet different objective function, such as current account balance, amount of biomass energy supply, and CO₂ emission. Most of biomass resources in a focused region e.g. wood biomass, livestock biomass, and crop residues are considered in the model. Conversion technologies considered are energy utilization technologies e.g. direct combustion and methane fermentation, and material utilization technologies e.g. composting and carbonization. Case study in Miyakojima, Okinawa prefecture, has been carried out for several objective functions and constraint conditions. Considering economics of the utilization system as a priority requirement, composting and combustion heat utilization are mainly chosen in the optimal system configuration. However gasification power plant and methane fermentation are included in optimal solutions, only when both biomass energy utilization and CO₂ reduction have been set as higher priorities. External benefit of CO₂ reduction has large impacts on the system configuration. Provided marginal external benefit of more than 50,000 JPY/t-C, external benefit becomes greater than the revenue from electricity and compost etc. Considering technological learning in the future, expensive technologies such as gasification power plant and methane fermentation will have economic feasibility as well as market competitiveness.