Cadmium (Cd) contaminated soil has threatened plant growth and human health. Rapeseed (Brassica napus L.), an ideal plant for phytoremediation, is an important source of edible vegetable oil, vegetable, animal fodder, green manure and biodiesel. For safe utilization of Cd polluted soil, physiological, biochemical, and molecular techniques have been used to understand mechanisms of Cd tolerance in B. napus. However, most of these researches have concentrated on vegetative and adult stages, just a few reports focus on the initial growth stage. Here, the partitioning of cadmium, gene expression level and activity of enzymatic antioxidants of H18 (tolerant genotype) and P9 (sensitive genotype) were investigated under 0 and 30 mg/L Cd stress at seedling establishment stage. Results shown that the radicle length of H18 and P9 under Cd stress were decreased by 30.33 (0.01 < P < 0.05) and 88.89% (P < 0.01) respectively. Cd concentration at cotyledon not radicle and hypocotyl in P9 was significantly higher than that in H18. The expression level of BnaHMA4c, which plays a key role in root-to-shoot translocation of Cd, was extremely higher in P9 than in H18 under both normal and Cd stress conditions. We also found that SOD, CAT and POD were more active in responding to Cd stress after 48 h, and the activity of SOD and CAT in H18 were higher than that in P9 at all observed time points. In conclusion, high activity of enzymatic antioxidants at initial Cd stress stage is the main detoxification mechanism in Cd-tolerant rapeseed, while the higher Cd transfer coefficient, driven by higher expression level of BnaHMA4c is the main mechanism for surviving radicle from initial Cd toxicity in Cd-sensitive rapeseed.