Biofuel supply chain design plays a critical role in facilitating the large-scale substitution of biofuel for traditional fossil fuels with a cost-effective and environmentally friendly manner towards sustainability. This paper proposes a multiobjective optimization model for a 4-layer biofuel supply chain network using mixed integer nonlinear programming while considering the benefits from economic, environmental, and societal aspects. The model can be used either to optimize an existing biofuel supply chain network or to guide the construction of a new biofuel supply chain network. The profit, the greenhouse gas emissions in transportation, and the market share of biofuel were set as targets for optimization. The selection of the participators at each layer, and the amount of the material flow between each pair of selected supplier and customer located at two adjacent layers were modeled as decision variables. The conventional weighted aggregation method was used to unify 3 objectives after normalization. Particle swarm optimization was used to solve this high-dimension multiobjective problem to obtain a near optimal solution. A numerical case study based on the state of Missouri in the United States was implemented to verify the effectiveness of the proposed model. The results of the case study illustrate that the benefits in terms of transportation emission, profit, and market share can be achieved simultaneously. Using the equal weights configuration in conventional weighted aggregation as an example, a 21% reduction of the transportation emission, a 33% increase of the profit, and a 2% augmentation of the market share were achieved compared to the benchmark scenario.