Brassica napus is the main source of edible vegetable oil in China, which plays an important role in the security of edible oil supply, and drought has seriously constrained the production of B. napus in China. Mining drought tolerance loci and candidate genes in B. napus germination will provide theoretical basis and technical support for breeding new drought-tolerant B. napus varieties. In this study, 145 B. napus germplasm resources were used for seed germination under normal and 15% PEG6000 conditions, respectively. The data of germination potential, seedling formation rate and germination index of different materials were investigated. The drought tolerance indicators were screened during germination and genome-wide association analysis was performed. The results showed that germination index could be used as an indicator of drought tolerance during the germination stage of B. napus. Total of 17 extreme drought-resistant and 9 extreme drought-sensitive germplasm were screened on the basis of germination index. A total of 14 SNP loci significantly associated with drought tolerance were detected by GWAS analysis of germination index using MLM (mixed linear model) in B. napus, which were distributed on two chromosomes, C07 and C09, with 11 loci on chromosome C07 and 3 loci on chromosome C09. Combing with the functional annotation of the candidate genes in the significantly associated SNP intervals and their expression data under different stresses, BnaC07G0290100ZS、BnaC07G0290500ZS and BnaC07G0290700ZS were significantly induced by drought stress, and it was hypothesized that BnaC07G0290100ZS、BnaC07G0290500ZS and BnaC07G0290700ZS are the key genes regulating drought tolerance in B. napus during germination stage.