Growing concerns about energy and the environment have led to worldwide use of bioenergy. Switching from food crops to biofuel crops is an option to meet the fast-growing need for biofuel feedstocks. This land use change consequently affects the ecosystem carbon balance. In this study, we used a biogeochemistry model, the Terrestrial Ecosystem Model, to evaluate the impacts of this change on the carbon balance, bioenergy production, and agricultural yield, assuming that several land use change scenarios from corn, soybean, and wheat to biofuel crops of switchgrass and Miscanthus will occur. We found that biofuel crops have much higher net primary production (NPP) than soybean and wheat crops. When food crops from current agricultural lands were changed to different biofuel crops, the national total NPP increased in all cases by a range of 0.14–0.88 Pg C yr−1, except while switching from corn to switchgrass when a decrease of 14% was observed. Miscanthus is more productive than switchgrass, producing about 2.5 times the NPP of switchgrass. The net carbon loss ranges from 1.0 to 6.3 Tg C yr−1 if food crops are changed to switchgrass, and from 0.4 to 6.7 Tg C yr−1 if changed to Miscanthus. The largest loss was observed when soybean crops were replaced with biofuel crops. Soil organic carbon increased significantly when land use changed, reaching 100 Mg C ha−1 in biofuel crop ecosystems. When switching from food crops to Miscanthus, the per unit area croplands produced a larger amount of ethanol than that of original food crops. In comparison, the land use change from wheat to Miscanthus produced more biomass and sequestrated more carbon. Our study suggests that Miscanthus could better serve as an energy crop than food crops or switchgrass, considering both economic and environmental benefits.