The new microalgae-to-biofuels chains for producing diesel and ethanol simultaneously are presented. The techno-economic analysis shows that the break-even prices of diesel and ethanol are estimated about US$0.49/kg and US$2.61/kg, respectively, the internal rate of return (IRR) is close to 29.21%, and the commercial prices and yield of products dominate the profitability of this project. According to life cycle analysis (LCA) standards, the life-cycle greenhouse gas (GHG) emissions for producing diesel and ethanol are 0.039 kg CO2-eq/MJ FAME and 0.112 kg CO2-eq/MJ EtOH, respectively. It is verified that the process integration of the heat recovery scheme, the entrainer recovery tower, and CO2 recycling can effectively reduce life-cycle GHG emissions of this design. Through a specific optimization algorithm under different lipid contents and 180 scenario combinations for the cultivation and pretreatment processes, the compromise solutions between the maximum total revenue and the minimum environmental impact can be found.