Leaf shape is a part of ideotype. Appropriate leaf rolling aids compact plant architecture. Oilseed is a crucial crop, but the genetic basis for leaf shape development in rapeseed (Brassica napus) is unclear, and no corresponding genetic improvement germplasm resources are available. We identified a dominant mutant, INSIDE-ROLLING LEAF1 (IRL1), in rapeseed with internal rolling of leaves due to abnormal mesophyll cell development. It had drooped siliques and a semi-dwarf stature, reducing of one to two effective branch numbers. Map-based cloning and complementary validation confirmed BnaC02G0201100ZS as causal gene IRL1. BnaC02G0201100ZS encodes LATERAL ORGAN BOUNDARIES DOMAIN6 (BnaC02.LBD6). Phenotypic variation of the irl1 mutant was due to an increase in BnaC02.LBD6 expression owing to a single nucleotide substitution at the DNA binding site in the promoter. Phenotype of plants overexpressing BnaC02.LBD6 was similar to that of the irl1 mutant. Haploid analysis showed a rare variation in BnaC02.LBD6 promoter, resulting in a unique phenotype in the irl1 mutant. Transcriptome analysis showed the differential expression of genes related to leaf adaxial–abaxial polarity development, secondary metabolic processes, and hormone signalling pathways. We provide novel insights into rapeseed: the genetic basis of variation in leaf characteristics and valuable genetic resources for plant architecture improvement.