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Hybrids between different subspecies of rice <i>Oryza</i> <i>sativa</i> L. commonly show hybrid sterility. Here we show that a widely planted commercial <i>japonica</i>/<i>GJ</i> variety, DHX2, exhibited hybrid sterility when crossing with other <i>GJ</i> varieties. Using the high-quality genome assembly, we identified three copies of the <i>Sc</i> gene in DHX2, whereas Nipponbare (Nip) had only one copy of <i>Sc</i>. Knocking out the extra copies of <i>Sc</i> in DHX2 significantly improved the pollen fertility of the F₁ plant of DHX2/Nip cross. The population structure analysis revealed that a slight introgression from Basmati1 might occur in the genome of DHX2. We demonstrated that both DHX2 and Basmati1 harbored three copies of <i>Sc</i>. Moreover, the introgression of <i>GS3</i> and <i>BADH2</i>/<i>fgr</i> from Basmati1 confers the slender and fragrance grain of DHX2. These results add to our understanding of the hybrid sterility of inter-subspecies and intra-subspecies and may provide a novel strategy for hybrid breeding.