Bio-fuel can be used to help transition from a petroleum-based society to a bio-based society. Ever since the China Development and Reform Commission suspended the approval of crop processing programs, second-generation bio-ethanol research and industrialization processes have attracted significant attention. In 2020, bio-ethanol production is predicted to reach 10 million tons. Currently, there are a few domestic enterprises that have established different scaled pilot or demonstration bases for cellulosic ethanol, which reduce the cost of ethanol by continuously improving pretreatment and hydrolysis techniques. In the next three years, these enterprises will realize large-scale commercial production. Given the practical problems in cellulosic ethanol plant construction and operation(e.g., marketing price variation and difficulties in feedstock collection), this paper began with the concept of a “whole-crop refinery” and presented a solution to the integration of industry and agriculture as well as multi-crop refining. This paper then took the whole-crop refining system of corn as an example and presented an analysis of the logistics, energy flow, and economical efficiency of the system. The results demonstrated that the integrated system could properly reduce the required fixed investments in production equipment,shared utilities, and wastewater treatment facilities, as well as reduction of energy consumption. Although the proposed system has several problems, it brings the long-term goal of large-scale commercial application closer than ever. Bio-fuel can be used to help transition from a petroleum-based society to a bio-based society. Ever since the China Development and Reform Commission suspended the approval of crop processing programs, second-generation bio-ethanol research and industrialization processes Currently, there are a few domestic enterprises that have established different scaled pilot or demonstration bases for cellulosic ethanol, which reduce the cost of ethanol by accelerated improves pretreatment and hydrolysis techniques. In the next three years, these enterprises will realize large-scale commercial production. Given the practical problems in cellulosic ethanol plant construction and operation (eg, marketing price variation and difficulties in feedstock collection), this paper began with the concept of a “whole-crop refinery ” and presented a solution to the integration of industry and agricu This paper then took the whole-crop refining system of corn as an example and presented an analysis of the logistics, energy flow, and economical efficiency of the system. The results demonstrated that the integrated system could properly reduce the required fixed investments in production equipment, shared utilities, and wastewater treatment facilities, as well as reduction of energy consumption. Although the proposed system has several problems, it brings the long-term goal of large-scale commercial application closer than ever .