Brassica napus is the main oil crop and the main source of edible vegetable oil in China. High-quality "double low" rapeseed is an important goal for the genetic breeding of Brassica napus. In this study, the content of erucic acid, oleic acid, and glucosinolate in 104 Brassica napus L. seeds has been analyzed by near-infrared method, and all materials have been genotyped by simplified genome technology(ddRADseq). Combining traits with genotype data, a Tassel mixed linear model has been used for genome-wide association analysis. The results showed that there was a significant positive correlation between erucic acid content and glucosinolates, and a significant negative correlation between oleic acid content and erucic acid and glucosinolates. The population structure analysis divided 104 materials into 4 subgroups. It was found that SNP markers significantly associated with erucic acid and the oleic acid content were mainly distributed on the A08 and C03 chromosomes, and markers associated with glucosinolate content were distributed on chromosomes A05, A02 and C09.