Carbon sequestration is an essential ecosystem service that second-generation energy crops can provide. To evaluate the ability of carbon sequestration of Miscanthus energy crops in the Loess Plateau of China, the yield and soil organic carbon (SOC) changes were measured for three Miscanthus species in the experimental field in Qingyang of the Gansu Province (QG). With the highest yield of the three species,Miscanthus lutarioriparius contributed to the largest increase of SOC, 0.57 t ha^− 1 yr^− 1, comparing to the field left unplanted. Through modeling M. lutarioriparius yield across the Loess Plateau, an average increase of SOC was estimated at 0.46 t ha^− 1 yr^− 1 for the entire region. Based on the measurements of SOC mineralization under various temperatures and moistures for soil samples taken from QG, a model was developed for estimating SOC mineralization rates across the Loess Plateau and resulted in an average of 1.11 t ha^− 1 yr^− 1. Combining the estimates from these models, the average of net carbon sequestration was calculated at a rate of 9.13 t ha^− 1 yr^− 1 in the Loess Plateau. These results suggested that the domestication and production of M. lutarioriparius hold a great potential for carbon sequestration and soil restoration in this heavily eroded region.