Key message <p>A core interaction network associated with cluster buds trait was discovered in <i>Brassica napus</i>, and indoleacetic acid-induced protein 8 (IAA8) might affect the shoot apical meristem (SAM) development through IAA8-ARF5 complex → DRN → CLV3 pathway.</p> Abstract <p><i>B. napus</i> is one of the important oilseed crops in China. However, the low level of mechanized production restricts the industry due to the infinite inflorescence characteristics of <i>B. napus</i>. Therefore, the cultivation of new varieties suitable for mechanized harvesting is one of the main objectives of rapeseed breeding. In this study, a screened natural mutant of <i>B. napus</i> with no branching or short branches in the bolting stage and a relatively shorter flowering period showed distinct traits of cluster buds and uniform maturity, which made it suitable for high-density cultivation and mechanized harvesting. Microscopic examination between the wild-type (WT) and the cluster buds mutant (<i>cbm</i>) lines was performed across developmental stages. The results showed that the SAM regions of the mutants were widened and exhibited multiple growth points due to the loss of apical dominance. Transcriptome sequencing of SAM regions in the WT and <i>cbm</i> lines identified 2497 differentially expressed genes (DEGs). Bulk segregant analysis (BSA) pinpointed five significant genomic regions associated with the cluster buds trait and identified 799 candidate genes. Finally, an interaction network associated with the cluster buds trait was constructed, within which IAA8 was revealed as a candidate gene to regulate the SAM development in <i>B. napus</i>. Taken together, the present study elucidates the potential molecular regulation mechanism of cluster buds trait and laid a solid theoretical foundation for the cultivation of new varieties suitable for close planting and mechanized harvesting in <i>B. napus</i>.</p>