Life cycle assessment of biodiesel produced from microalgae showed that the pure energy output was negative by the route of biodiesel (FAME), if the biodiesel was produced from high moisture content microalgae slurry by dry, cell disruption, solvent extraction of lipids, and transesterification. Therefore, passive choices are that mathane or bioethanol is obtained by anerobic digestion of microalgae slurry or their hydrolysate, or microalgae based bio-oils are obtained by fast pyrolysis and microwave assisted pyrolysis of dried microalgae biomass, or microalgae based bio-oils or syngas by hydrothermal treatment of microalgae slurry. Although the high heating value（HHV）of microalgae based bio-oils are much higher than lignocellulosic bio-oils, it can still not meet the demand of transportation liquid fuel due to its high nitrogen content, high oxygen content and instability. Possessing superiority of dehydration, oil extraction, protein and polysaccharide separation, or even in situ biodiesel production from high moisture content microalgae slurry, subcritical water treatment may become the prior research field of downstream processing technology for microalgae biofuels today. The most challenging research field is to know how to extract lipids, separate cytochrome, protein, polysaccharide from high moisture content microalgae slurry simultaneously under very mild reaction condition of enzymolysis, so that most of the functional components of the microalgae will be saved for value added comprehensive utilization. Last and key technology that may guide microalgae fuel to commercialization is how to manufacture renewable and high quality hydrocarbon diesel effectively from microalgae oil or its soap by microwave polarization decarboxylation.