Intending to contribute to sustainable agriculture by “New Green Revolution,” we developed a large-grain/semidwarf isogenic line “Koshihikari sd1GW2” that incorporates both the large-grain gene GW2 and semidwarf gene sd1. GW2 homozygous B3F2 plant with the genomic background of Koshihikari was backcrossed twice with “Koshihikari sd1.” Koshihikari sd1GW2 fixed in BC5F3 was found to be 12.6 cm shorter than Koshihikari. Whole-genome sequencing proved one deletion in GW2 at 8,147,416 bp on chromosome 2 and the SNPs in sd1 at 38,267,510 bp on chromosome 1. The size of the DNA fragments integrated with each gene was determined as the distance between both ends of SNP clusters. Through the backcrossing from BC4 to BC5, the DNA fragment integrated with GW2 decreased by 148,139 bp. The thousand-grain weight of Koshihikari sd1GW2 (27.8 g) was 18% greater than that of Koshihikari (23.6 g), and the grain yield of Koshihikari sd1GW2 (42.6 kg/a) was 0.5% higher than that of Koshihikari (42.4 kg/a). Our results suggested that Koshihikari sd1GW2 will be less susceptible to lodging by typhoons, cyclones, and heavy rainfall, ordinarily a concern in heavier panicle weight cultivars. We successfully integrated GW2 with sd1 for the first time, specifically in the genome of the leading, globally produced Japonica cultivar Koshihikari.