This paper presents a robust optimization method to deal with the deep uncertainty of a green biomass-to-bioenergy supply chain system design. The proposed model is triggered to minimize the total costs including establishing facilities costs, material flow costs, and inventory holding costs and to maximize carbon trade. In the proposed model, carbon dioxide emissions (CO2-equivalent) of all involved processes are calculated through Ecoindicator 99 method employing SimaPro software. Due to a lack of historical information about the parameters of the proposed model, set-induced robust optimization method is utilized to model the deep uncertainty of parameters. The proposed model is implemented in a real case in Iran. The results justify the efficiency of the proposed model in designing a green biodiesel supply chain network.