Oryza rufipogon served as an important rice germplasm which harbors excellent yield and stress tolerance genes that have been lost or weakened in cultivated rice. Within this study, a set of introgression lines with chromosome segments derived from Chaling wild rice were used for genetic analysis and QTL identification. Two-hundred sixteen polymorphic markers evenly distributed across the 12 chromosomes were deployed for genotyping. 87.89% of the Chaling wild rice genomes were detected. Averagely, 24 introgression segments were found in each introgression line, and the genetic distance of each segment was accounting for about 16.1 cM. By taking use of phenotypic datasets from two environments, eighteen QTLs on six yield traits were identified. Especially, a QTL associating with grain width on chromosome 6 was found in two environments. Furthermore, five QTLs related to cold tolerance at the germination stage were detected. Taken together, these introgression lines served as elite gene resources with a potential for rice breeding.