A rice F2 population was obtained from a hybrid cross of the indica restorer line CG133R with high amylose content and the glutinous rice variety javanica 22, which was as materials. The variation and their correlation between the cooking and eating quality indices and starch RVA characteristic values were analyzed and the genetics of the major genes (Wx and SSII-3) controlling the physicochemical indexes in the F2 population were examined. The results indicated that the physicochemical indexes and RVA profile characteristics had great variation in F2 population, setback with the maximum variation, followed by gel consistency and amylose content; correlation of physicochemical indexes of materials with high amylose content were not significant with RVA profile characteristics. RVA profile characteristics in materials with medium, low amylose content and glutinous rice groups had significant or extremely significant correlation with the physical and chemical indices. In materials with medium and low amylose content, there also had significant or extremely significant correlation with gelatinization temperature (GT). Separation of Wx and SSII-3 genes in F2 population was detected using molecular marker and showed that the two molecular markers existed partial separation and deviated to two parent types, respectively. There was more variation in the F2 population except for the materials with high amylose content. RVA profile characteristics could be used for assisted-selection for quality rice breeding.