The aviation industry has some emission policy initiatives in place to reduce its carbon emissions. European Union (EU) has implemented the Emissions Trading Scheme (ETS) since 2012 for intra-European commercial flights. In response, airlines started to explore various mean, including alternative jet fuels. However, it is not clear how similar policy schemes would affect domestic carbon emissions if implemented in the United States. This paper integrates U.S. airlines operations optimization and multi-feedstock biojet fuels life cycle assessment model to simulate decisions of bio-jet fuel and commercial aviation industry responding to an emission policy similar to ETS.