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Pyramiding of quantitative trait loci (QTLs) is a powerful approach in breeding super-high-yield varieties. However, the performance of QTLs in improving rice yield varies with specific genetic backgrounds. In a previous study, we employed the CRISPR/Cas9 system to target three yield-related genes, <i>gn1a</i>, <i>gs3</i>, and <i>ipa1</i> in japonica ‘Zhonghua 11’, mutants of which featured large panicle, big grain, few sterile tillers, and thicker culm, respectively. In this paper, four pyramided lines, including <i>gn1a-gs3</i>, <i>gn1a-ipa1</i>, <i>gs3-ipa1</i>, and <i>gn1a-gs3-ipa1</i>, were further generated by conventional cross-breeding to be tested. Agronomic traits analysis showed that: (1) the stacking lines carried large panicles with an increased spikelet number in the main panicle or panicle; (2) the grain weight of the stacking lines, especially <i>gs3-ipa1</i> and <i>gn1a-gs3-ipa1,</i> were heavier than those in single mutants; (3) both <i>gn1a-gs3</i> and <i>gs3-ipa1</i> produced more grain yield per plant than single mutant lines; (4) pyramided lines were higher than single mutants and transcriptome analysis found improved expression levels of genes related to lipid, amino acid, and carbohydrate transport and metabolism in lines pyramiding three mutant alleles, possibly as a result of complementary and additive effects. Accordingly, the alteration of gene-expression patterns relating to hormone signaling, plant growth, and seed size control was characterized in pyramided lines. The present study not only investigates the effects of pyramiding genes, but also may provide an efficient strategy for breeding super-high-yield rice by reducing the time cost of developing pyramided lines.