Therefore, this paper will address the potential harmful ecological services impacts (HESI) due to large-scale production and usage of biofuels. To study this complex and challenging issue, this paper, taking the corn-ethanol production as an example, first conducted the life-cycle HESI analysis for biofuel production, which covers every stage of biofuel material flow chain. Then, emergy-based input-output analysis (IOA) method is employed to identify the proposed HESI index, such that negative ecological services impacts could be clearly quantified. It demonstrates that current biofuel thrusts for renewable energy are most likely shortsighted behaviors that may not be viable in long-term sustainability. Finally, based on the developed methodology, several suggestions for avoiding HESI from biofuel productions are discussed.