In Brassica napus, hypocotyl elongation under shade conditions poses a significant challenge in intensive agricultural systems, particularly in rice-rapeseed rotation regimes where straw mulching reduces light quality. However, the genetic basis of light-mediated hypocotyl growth responses in B. napus remains poorly understood. In this study, hypocotyl lengths were measured in a panel of 267 diverse rapeseed accessions under five light conditions including white, red, far-red, blue light, and complete darkness. Substantial phenotypic variation was observed among accessions and treatments, with red light exhibiting the weakest inhibitory effect on elongation, and white light showing the strongest suppression. Genome-wide association studies (GWAS) (−log₁₀ (p) > 4.5) identified numerous significant SNPs associated with light response, highlighting candidate genes such as KAN1, ILL2, VQ18, HDA15, and HAT3 involved in photomorphogenesis and hormonal signaling pathways. These findings elucidate the polygenic control of light responsiveness in B. napus and provide molecular targets for breeding shade-tolerant varieties to enhance crop resilience under dense planting and straw mulching systems.