The efficiency of supply chain system of lignocellulosic biomass (LCB) feedstock is crucial to the development of the cellulosic biofuel industry. Moreover, the potential environmental impact of LCB feedstock transportation has also received increasing attention lately. This study first applied a spatial-oriented mixed-integer mathematical programming model linked to a GIS resource model to generate a least-cost solution of alternative typical feedstock supply chain systems for a potential commercial scale biorefinery per year in east, central and west Tennessee. The EPA’s MOVES model was then used to estimate the baseline emissions for 2010 in the study region and additional emissions generated from hauling feedstock. Results showed that switchgrass is more suitable than energy sorghum for biofuel production in Tennessee based on feedstock plant-gate cost and hauling emissions. Also, the large square bale system outperformed the large round bale system in both economic and environmental indicators. Finally, the biorefinery with the most economic feedstock cost and the least feedstock hauling emission is suggested to be sited in Robertson County, TN. The emissions of NOx, CO2, PM10, and PM2.5 from feedstock hauling in related counties increased by 0.12%, 0.04%, 0.15%, and 0.18%, respectively, when comparing with the emissions produced by existing overall traffics.