[Objective] The study aims to reveal the genetic loci and candidate genes associated with the dwarf trait in Brassica napus, thereby laying a foundation for breeding to improve the plant height and lodging resistant of B. napus. [Methods] Rapeseed dwarf stem DW1 was used to cross with tall stem lines WH14 and WH20, respectively, and the F1 and F2 generations were used to analyze the genetic mechanism behind the of dwarf trait. Meanwhile, two DNA mixed pools, one from extremely tall and the other from dwarf stem lines, constructed from F2 segregated population of dwarf stem DW1 and tall stem WH20 hybrid combination were sequenced and analyzed base on BSA-seq technology, and the significant association regions and candidate genes associated with dwarf trait were identified. [Results] (1) The dwarf trait of B. napus DW1 was one quality trait and was controlled by one pair of incomplete dominant genes. (2) Twenty-two genomic regions significantly associated with dwarf trait were identified within the 21.78—23.88 Mb region on chromosome A06, with the maximum interval of 46.71 kb and the minimum interval of 0.64 kb. (3) Potential candidate genes, including BnaA06g27050D, BnaA06g34100D, BnaA06g34810D, BnaA06g35080D and BnaA06g36480D, were identified in significantly associated regions on chromosome A06, which were related to the regulation of plant auxin and gibberellin signal transduction, respectively. [Conclusion] The dwarf trait herein is one quality trait controlled by one pair of incomplete genes. One significantly associated regions were identified in the genomic region from 21.78 M to 23.88 Mb on chromosome A06. Five candidate genes within the significantly associated regions were identified and invloved in the regulation of plant auxin synthesis and gibberellin signal transduction.