In this paper we present a life cycle assessment (LCA) based biofuel supply chain model with multi-conversion pathways. This model was formulated as a mixed integer linear programming (MILP) problem which took economic, energy, and environmental criteria (3E) into consideration. The economic objective was measured by the total annual profit. The energy objective was measured by using the average fossil energy input per megajoule (MJ) of biofuel. The environmental objective was measured by greenhouse gas (GHG) emissions per MJ of biofuel. After carefully consideration of the current situation in China, we chose to examine three conversion pathways: bio-ethanol (BE), bio-methanol (BM) and bio-diesel (BD). LCA was integrated to a multi-objective supply chain model by dividing each pathway into several individual parts and analyzing each part. The multi-objective MILP problem was solved using a epsilon-constraint method by defining the total annual profit as the optimization objective and assigning the average fossil energy input per MJ biofuel and GHG emissions per MJ biofuel as constraints. This model was then used to design an experimental biofuel supply chain for China. A surface of the Pareto optimal solutions was obtained by linear interpolation of the non-inferior solutions. The optimal results included the choice of optimal conversion pathway, biomass type, biomass locations, facility locations, and network topology structure in the biofuel supply chain. Distributed and centralized systems were also factored into our experimental system design. In addition, the influence of price change on the optimal solutions was investigated. The optimal solutions obtained in this study reveal a tradeoff between the impact of the 3E criteria. These results indicate that our model will be extremely useful for the design and planning of biofuel supply chains in China. (C) 2014 Elsevier Ltd. All rights reserved.