Suberin lamellae in endodermis provide the mineral elements uptake barrier to regulate mineral nutrients and heavy metal import through endodermis cells. However, the regulation mechanism of suberin on heavy metal uptake in root of Brassica napus remains unclear. In the present study, overexpression of BnaFAX1.1, a plastid membrane localized protein involved in oil accumulation, in B. napus enhanced the length of fully suberized zone, not suberin patchy zone and increased suberin monomers contents in the roots. Distribution of suberized zone was significantly strengthened by Cd stress. Interestingly, suberin patchy zone was decreased, and number of lateral roots was increased in the BnaFAX1.1 overexpression line under Cd stress condition. Moreover, we found that suberin lamellae can act as a barrier to block the absorption of heavy metal Cd by NMT and ICP-OES in root of B. napus. As a nonspecific barrier, the absorption of other ions, such as Cu, Mn, P, were also weakened by the suberin lamellae. The present study revealed that BnaFAX1.1 is involved in suberin monomers accumulation in root of B. napus, which regulated suberin amount in the endodermis and regulated mineral nutrient and heavy metal uptake.