The current challenge of drop-in jet fuel should couple the reduction of GHGs emission in whole life cycle with economic competitiveness and achieving performance as same as traditional jet fuel without reducing safe service life in engine and aircraft. From the insight of GHGs reduction, the whole life cycle, including sustainable feedstock, refining process integration and low emission in combustion are optimized for reduction in energy input and emission output. From the insight of airworthiness in aero-engine and aircraft, a certification process is achieved by extracting safety criteria from the "history experience" of petroleum-based jet fuel as the source and to predict the aero-engine safety implications of alternative aviation fuels as the target by "similar analogy". The critical key parameters have been extracted by fundamental process related with safety and performance on achieving the duty of engine in the whole flight envelop. Alternative jet fuel can be qualified for certifying drop-in jet fuel and accordingly confirm with identical safe service life in engine and aircraft by analogizing the boundaries of critical key parameters with petroleum-based jet fuel. The critical parameters thereof, including carbon distribution and classification as well as C/H ratio, can conduct directly for feedstock choice and refining process modification. Accordingly, a process of refining algae-based jet fuel was modified coupling the requirement of GHGs reduction in life cycle with airworthiness in aero-engine and aircraft. Based on process integration to connect upstream feedstock to downstream combustion outcomes of alternative jet biofuel and co-product, GHGs in fuel stage deduced further by co-product and nutrient recovery in spite of additional separation process.