SUMMARY Plant height (PH) is an important trait affecting the plant architecture, seed yield, and harvest index. However, the molecular mechanisms underlying PH heterosis remain unclear. In addition, useful PH‐related genes must be urgently identified to facilitate ideal plant architecture breeding in rice (Oryza sativa L.). In the present study, to explore rice quantitative trait loci (QTLs) and heterosis‐related loci of PH in rice, we developed a high‐generation (>F15) population of 272 recombinant inbred lines (RIL) from a cross of two elite varieties, Luohui 9 (indica/xian) × RPY geng (japonica/geng), and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA indica and Z7A japonica). Using deep resequencing data, a high‐density genetic map containing 4758 bin markers was constructed, with a total map distance of 2356.41 cM. Finally, 31 PH‐related QTLs for different PH component lengths or tiller numbers across five seasons were identified. Two major environment‐specific PH QTLs were stably detected in Hainan (qPH‐3.1) or Hubei (qPH‐5.1), which have undergone significant functional alterations in rice with changes in geographical environment. Based on comparative genomics, gene function annotation, homolog identification, and existing literature (pioneering studies), candidate genes for multiple QTLs were fine‐mapped, and the candidate genes qPH‐3.1 and qPH‐5.1 for PH were further validated using CRISPR–Cas9 gene editing. Specifically, qPH‐3.1 was characterized as a pleiotropic gene, and the qPH‐3.1 knockout line showed reduced PH, delayed heading, a decreased seed setting rate, and increased tiller numbers. Importantly, 10 PH heterosis‐related QTLs were identified in the testcross populations, and a better‐parent heterosis locus (qBPH‐5.2) completely covered qPH‐5.1. Furthermore, the cross results of fixed‐genotype RILs verified the dominant effects of qPH‐3.1 and qPH‐5.1. Together, these findings further our understanding of the genetic mechanisms of PH and offer multiple highly reliable gene targets for breeding rice varieties with ideal architecture and high yield potential in the immediate future. Significance Statement In the present study we constructed a high‐density genetic map containing 4758 bin markers of a high‐generation recombinant inbred line population from a cross of two elite rice (Oryza sativa L.) varieties, Luohui 9 (indica/xian) × RPY geng (japonica/geng). Two major environment‐specific QTLs of plant height were discovered and experimentally validated.