This paper presents an emergy-based accounting for the whole production chain of biodiesel made from Jatropha Curcas L.(JCL) oil combined with material flow analysis. The total demand and output method which considers renewable resources, nonrenewable resources and purchased resources is employed to establish an emergy indicator framework and evaluate the eco-efficiency and sustainability of the process including cropping, transportation, extraction, production and wastewater treatment. The results show that emergy yield ratio (EYR) is 1.85, environmental load ratio (ELR) is 6.84, and the emergy sustainability index (ESI) is 0.271. The results are also compared with those of the biodiesel made from soy oil and bioethanol made from wheat, indicating that the biodiesel production process with JCL oil as raw materials is associated with higher yield, dependences on the environment, and sustainable level, which may be more suitable to be developed.