Seed density within per silique will affect seed per silique (the constituent elements of rapeseed yield) , which have a direct or indirect effect on rapeseed yield.In this study, a population of 213 Brassica napus accessions (or lines) were collected from different genetic backgrounds and geographical origins with the Brassica 60 K Illumina Infinium SNP array for assess population structure, relative kinship and linkage disequilibrium. Then the optimal model of each trait was selected array for genome-wide association analysis of the silique density of seed density within per silique and its related traits. A total of 10 SNPs were detected to be with significant association with the seed density within per silique and its related traits in 2016 year. 2 SNP sites associated with seed density within per silique were detected, explaining the phenotypic variation of 9.94% and 11.17%, respectively. 6 SNP sites associated with valid silique length were detected, and Single loci can explain the phenotypic variation of 9.81%-12.17% of the phenotypic variation. 2 SNP sites associated with seed per silique were detected, explaining the phenotypic variation of 10.44% and 10.87%, respectively. According to analyzing the genes information of the LD region sequence associated with the SNP site, we screened 16 candidate genes associated with silique density of major inflorescence and its related traits. KMD4 and UGT76C2 genes are involved in the regulation of cytokinin, and the genes i.e. AGL104 and ADC2 was found to be related to seed formation process. Other genes, such as MCCB、NGA2 and MATE, are involved in the growth and development of lateral organs, when abnormal expression lead to lateral organ variants. Two candidate genes ADC and UGT76C2, which overlapped in seed density within per silique and seed per silique, tended to have pleiotropism.