FACE (free air carbon dioxide enrichment) technology may provide a means by which the environment around growing plants can be modified to realistically simulate the concentration of atmospheric CO2 in the future. The plant growth and its yield of plant species can be enhanced under FACE. Identification of genomic regions influencing the response of yield and its components to elevated CO2 will be useful for understanding the genetics of active response to changed CO2 environment and developing higher yield cultivars, which will be adapted to future enriched atmospheric CO2 environment. A mapping population of 65 indica (IR24) chromosome segment substitution lines (CSSLs) in japonica (Asominori) background and their parents were used to detect QTLs for yield and its components, e. g. number of fertile tillers per plant (FT), 1000-grain weight (TGW), number of grains per panicle (GP) and grain yield per plant (GY) under FACE (200 micromol CO2/mol above current levels) and current CO2 concentration (Ambient, about 370 micromol CO2/mol) in the field experiment. The results showed that, GY, GP and FT of two parents under FACE were significant greater than that under Ambient. The transgressive segregation of the four traits was observed in the CSSLs population under both FACE and Ambient. A total of 20 QTLs for the four traits were detected on chromosome 1, 2, 4, 6, 7, 9 and 12 with LOD (Log10-likelihood ratio) of QTLs ranging from 2.5 to 5.7. Three QTLs were detected under both FACE and Ambient. However,other QTLs were detected only under one level of CO2, which indicated that these loci were sensitive to CO2 concentration. Additionally, two QTLs qFT12 and qGP4 were found for the QTL x Environment (QE) interaction effects. It is suggested that there is a high possibility to improve the yield of rice under elevated CO2 through marker-assisted selection.