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As a desirable agricultural trait, multi-inflorescence (MI) fulfills the requirement of mechanized harvesting and yield increase in rapeseed (<i>Brassica napus</i> L.). However, the genetic mechanism underlying the multi-inflorescence trait remain poorly understood. We previously identified a difference of one pair of dominant genes between the two mapping parental materials. In this study, phenotype and expression analysis indicated that the imbalance of the <i>CLAVATA</i> (<i>CLV</i>)-<i>WUSCHEL</i> (<i>WUS</i>) feedback loop may contribute to the abnormal development of the shoot apical meristem (SAM). <i>BnaMI</i> was fine-mapped to a 55 kb genomic region combining with genotype and phenotype of 5768 BCF₁ individuals using a traditional mapping approach. Through comparative and expression analyses, combined with the annotation in <i>Arabidopsis</i>, five genes in this interval were identified as candidate genes. The present findings may provide assistance in functional analysis of the mechanism associated with multi-inflorescence and yield increase in rapeseed.