Utilization of Biofuel Energy Policy in gasoline and diesel vehicles in Thailand was related to a partially blended portion of dehydrated ethanol and biodiesel in fossil fuel. It could directly reduce fossil energy in the vehicle tank and GHG emitted from the engine combustion. In the other hands, embodied energy in the upstream energy chain and the footprints of GHG emissions inherent before entering the driving process were not considered. An impartial comparison between two different energy systems requires life cycle analysis (LCA), including embodied energy and GHG emissions in related input materials and services, energy production, distribution, and transportation. The aim of this research is to provide comparisons of net energy saving and GHG emissions mitigation from these two different transportation energy policies in term of full energy chain analysis, appeared in case studies. The data of Embodied Energy and GHG Emissions for LCA from 180 commodities as of the year 2008 are provided in the prior result of the study, derived from economic Input-Output Analysis (IOA). The data could be used as an inventory data for any LCA study where embodied energy and GHG emissions in deeper subprocesses could not be surveyed by process analysis (PCA). The boundary layer of LCA study could be extended to the infinite subprocess. The Input-output (I-O) model was derived from 2000 I-O table and 1998 energy I-O data, but their important energy structure were updated in the power sector as of the recent year of the power sector fuel mix. Results of the cases of LCA on ethanol and biodiesel were found that GHG mitigation from the biofuel policies cause small impact to fossil energy saving and GHG mitigation due to small portion of biofuel mixed in the fuels. However, increasing percentage of the energy saving or GHG is not as high as the increasing percentage of the biofuel mixed in the fuel, since direct emissions from the high portion of fossil fuel persists and indirect emissions exists. It is recommended to encourage the energy savings and GHG emission reductions in significant upstream process, particularly in the power sector, where impact to other commodities is very high.