Soil salinization has become one of the important factors affecting the sustainable development of agriculture. Among them, the soda-alkali soil composed of sodium carbonate (Na2CO3) has a more serious impact on crops. In this study, 175 Brassica napus accessions from different sources were used as materials, combined with Brassica 60 K SNP chip data, and the root length traits of Brassica napus during germination under Na2CO3 stress (0.15%) and control conditions were analyzed for genome-wide association (GWAS). GWAS analysis detected that 5 SNPs were significantly related to root length traits under stress conditions; a single SNP could explain 10.22–12.01% of the phenotypic variation. A total of 15 candidate genes related to Na2CO3 stress resistance were identified upstream and downstream of significant SNPs, including cation exchange protein genes (CAX1), members of the zinc finger protein family (ZFHD1), peroxidase family proteins (POD), and transcription factors (MYB family and WRKY family), etc. The expression analysis of 5 candidate genes in extreme phenotypic materials showed that BnaA04g21850D (CAX1) and BnaA06g24040D (ACX5) were induced by Na2CO3 stress in both materials; BnaA06g31200D (ZFHD1) and BnaC02g37590D (MYB60) were up-regulated expression in sensitive materials; BnaA04g21990D (POD) was up-regulated expression in alkali-tolerant materials, indicating that these candidate genes may be involved in the process of rapeseed response to Na2CO3 stress. This study can provide a reference for in-depth analysis of the molecular mechanism of Na2CO3 stress resistance in rapeseed.