This paper presents a life cycle assessment (LCA) based biofuel supply chain (SC) analysis framework which enables the study of economic, energy and environmental (3E) performances by using multi-objective optimization. The economic objective is measured by the total annual profit, the energy objective is measured by the average fossil energy (FE) inputs per MJ biofuel and the environmental objective is measured by greenhouse gas (GHG) emissions per MJ biofuel. A multi-objective linear fractional programming (MOLFP) model with multi-conversion pathways is formulated based on the framework and is solved by using the e-constraint method. The MOLFP problem is turned into a mixed integer linear programming (MILP) problem by setting up the total annual profit as the optimization objective and the average FE inputs per MJ biofuel and GHG emissions per MJ biofuel as constraints. In the case study, this model is used to design an experimental biofuel supply chain in China. A set of the weekly Pareto optimal solutions is obtained. Each non-inferior solution indicates the optimal locations and the amount of biomass produced, locations and capacities of conversion factories, locations and amount of biofuel being supplied in final markets and the flow of mass through the supply chain network (SCN). As the model reveals trade-offs among 3E criteria, we think the framework can be a good support tool of decision for the design of biofuel SC.