Abscisic acid (ABA) plays a crucial role in plant response to abiotic stress. However, the molecular mechanism by which ABA inhibits the absorption of cadmium (Cd) in Brassica napus seedlings remains to be elucidated. In this study, “Youfei 1” of Brassica napus L. was used as experimental material, and 10 μmol/L Cd2+ was added to Hoagland solution to simulate cadmium stress. The effects of 5 μmol/L ABA on photosynthetic rate, chlorophyll, carotenoid contents in leaves, cadmium content in above/below ground parts of seedlings and differential expression genes of rapeseed under cadmium stress were analyzed. The results showed that the transpiration rate and stomatal conductance of rapeseed leaves were significantly increased, the contents of chlorophyll and carotenoid were decreased, and the contents of cadmium in aboveground and underground parts were significantly increased under Cd stress compared with the control group. The application of ABA could effectively reduce the leaf transpiration rate and stomatal conductance, as well as the contents of cadmium in aboveground and underground parts, and significantly increase the contents of chlorophyll a and carotenoid. Through transcriptome sequencing to screen differentially expressed genes, 514 genes were identified as upregulated and 431 genes as downregulated by ABA in response to Cd stress in Youfei 1. Gene Ontology (GO) functional enrichment revealed that differentially expressed genes were enriched in categories such as hemicellulose metabolism, oxidoreductase activity, phenolic compound metabolism, cell wall macromolecule metabolism, and system acquired resistance. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that differentially expressed genes were heavily enriched in pathways such as sucrose and starch metabolism, secondary metabolite biosynthesis, metabolic pathways, and the MAPK signaling pathway, etc. Further analysis of the different expression of genes related to lignin and hemicellulose metabolism. The results provided a reference for the regulation of physiological mechanism and molecular breeding in rapeseed under cadmium stress by exogenous ABA.