In order to improve rice quality combining ability of parental lines more efficiently in hybrid japonica rice(Oryza sativa L.), SSR molecular marker fragment genotypes of elite combining ability for eight quality traits were identified by analyzing the data of combining ability and SSR markers in eleven cytoplasmic male sterile(CMS) lines and nine restorer lines. The eight quality traits investigated were brown rice rate (BRR), milled rice rate (MRR), head rice rate (HRR), percentage of chalky grain, chalkiness degree, alkali spreading value (ASV), gel consistency, and amylose contents. The 11 CMS lines and 9 restorer lines were genotyped using 152 pairs of SSR primers. Combining ability analysis was conducted using the data of 99 F₁s made with NCII genetic design (11 CMS lines×9 restorer lines). A total of 49 SSR molecular marker fragment genotypes involving 27 molecular marker fragments were significantly associated with general combining ability of the 8 quality traits. 31 SSR molecular marker fragment genotypes on 14 chromosome arms were associated with elite combining ability for quality traits of parents; the remaining 18 molecular marker fragment genotypes were associated with unfavorable combining ability of quality traits of parents. Among the 49 molecular marker fragment genotypes, two were co-associated with four quality traits of parents, and two were each co-associated with three quality traits of parents, and eight were each co-associated with two quality traits of parents. The molecular marker fragment genotype RM542-80/105 on the long arm of chromosome 7 increased alkali spreading value in F₁ by 37.0%, RM246-95/105 on the short arm of chromosome 1 decreased amylose contents in F₁ by 23.8%, RM3754-80/90 on the long arm of the chromosome 8 increased the traits of BRR, MRR, HRR and ASV in F₁ by 1.1%, 2.0%, 2.4% and 43.6%, respectively. The molecular marker fragment genotypes could be directly used for improving general combining ability of grain quality traits of parents in japonica rice.