The present study conducted QTL (quantitative trait locus) mapping using F2 and F2:3 generations derived from a cross between an overwintering cultivated rice Nuodao89-1 and Shuhui527, to identify potential yield component related QTLs. A total of 37 QTLs were detected across all chromosome except chromosome 7, with LOD values ranging from 3.10 to 12.67. Three QTLs including qTGW3.1, qTGW6.1 and qNEG9.1 were repeatedly detected in both generations. qTGW3.1 was from Nuodao89-1, a total of 46 functionalgenes involved in 229 gene ontology terms were identified within its locus. Six QTL clusters were founded and corresponding agronomic traits of those QTLs showed highly significant correlation. Three types of epistatic interaction including 47 epistatic QTL pairs for eight yield component traits were detected, but the epistatic QTLs was not so important in controlling the genetic expression of the yield-related Nuodao89-1 as the additive QTLs. Overall, this research provides a theoretical basis for the mining of yield-related genes from over-wintering cultivated rice.