Good germination and seedling vigour are major breeding targets in winter oilseed rape (Brassica napus), because seedling vigour and prewinter crop establishment are closely associated with postwinter growth and yield. Here, we identified quantitative trait loci (QTL) related to germination, seedling vigour and seedling‐regulated hormones in a doubled haploid (DH) mapping population from a cross between winter oilseed rape parents with high vigour (Express 617) and low vigour (1012‐98). By phenotyping in a climate‐controlled glasshouse, we identified a total of 13 QTL on nine chromosomes for germination and seedling‐related traits at 7 and 14 days after sowing (DAS), explaining up to 11.2% of the phenotypic variation for seedling vigour. Forty‐seven metabolic QTL on 15 chromosomes were identified for auxin, abscisic acid (ABA) and dihydrophaseic acid (DPA) at 5 and 12 DAS, explaining up to 49.4% of phenotypic variation in seedling hormone composition. Multitrait QTL hot spots contribute to our understanding of the genetics and metabolomics of germination and seeding vigour in B. napus, and represent potential targets to breed high‐vigour cultivars.