The panicle erectness (PE) japonica cultivars have been widely planted in China. However, the relatively low yield level per plant and inferior eating and cooking quality of PE japonica cultivars are needed to improve further. In present study, a typical PE japonica cultivar, Nanjing 46, was selected as target for improving yield and grain quality by the way of introgression of Gn1a, qPC-1, and sd1 allele conferring grain number, grain protein content (GPC), and plant height, respectively. We obtained the improved lines containing Gn1a, qPC-1-sd1, and qPC-1-sd1-Gn1a through consecutive backcrossing with the help of gene-tagged markers. Agronomic and quality trait analysis showed that the introgression of Gn1a allele exhibited a positive effect on many panicle characters, including longer panicle length and grain length, more grain numbers per panicle, finally resulting in an increased grain yield. The introgression of sd1 allele could significantly reduce the plant height, and no negative effects were found on the panicle performance of the plants containing Gn1a allele. The introgression of qPC-1 could significantly reduce GPC, then increase rice palatability based on the RVA analysis. The result indicated that it is feasible to improve rice yield and grain quality of PE japonica cultivars by replacing these three favorable alleles simultaneously. This strategy could also be applied in the improvement of common japonica cultivars.