The production of energy via fermentation is an important method to develop the renewable energy sources. Due to adverse environmental factors such as higher temperature, higher osmotic pressure and solvent toxicity in the process of industrial production, the physiological functions of producing strains were often changed, then reducing biotransformation efficiency. Therefore, obtaining excellent strains with higher yield and higher solvent resistance is of great significance for the current ethanol and butanol industrial fermentation. In this paper, we propose to discuss the ethanol and butanol producing strains, and the current breeding methods for improving ethanol and butanol fermentation performance were systematically reviewed. The opportunities and challenges in the production process of ethanol and butanol were also discussed.