Nowadays human beings face the crisis and challenge of environmental pollution and energy shortage. The green treatment of low-quality biomass (such as wastewater, waste gas and solid waste), and development of microalgae biofuel are hot spots of pollution treatment and new energy development respectively. Base on the coupling system of microalgae cultivation by slurry (the product of anaerobic digestion of low-quality biomass) and biofuel production by microalgae, it is most likely to achieve an organic integration of the two hot spots, obtaining alternative liquid fuel and realizing slurry purification finally. In addition, there are added benefits can be obtained from the system, such as some high value-added products, animal feed, organic fertilizer, high-absorption materials, and so on. In this paper, combining the latest research advances of our research group, we made a brief analysis of the feasibility of microalgae cultivation by slurry, the characteristics of microalgae cultivation and lipid accumulation, the refining technologies of high calorific value fuel from microalgae, etc., and prospected the coupling system of low-quality biomass treatment and microalgae biofuel production.