To identify the key barrier parts and relevant elements during Cd/As transport into brown rice, 16 elements were measured in 14 different parts of 21 rice genotypes; moreover, transcriptomic of different nodes was analyzed. Cd/As contents in root and nodes were significantly higher than those other parts. Node I had the highest Cd content among nodes, leading an increase in gene expressions involved in glycolytic and Cd detoxification. The Cu/Zn/Co distribution and transport to various parts was similar to that of Cd, and Fe/Sb distribution and transport to various parts was similar to that of As. Moreover, Cu/Zn/Co/Mg was correlated with Cd in root and nodes, as well as Fe with As. Besides, the ionomic profile showed the different parts of an organ were closely related, and the spatial distribution of different organs was consistent with the growth morphology of rice. Therefore, root and nodes are two key barriers to Cd/As transport into brown rice. Moreover, Node I has the highest Cd accumulation capacities among nodes. The ionomic profile reflects relationships among plant parts and correlations between the elements, suggesting that nodes are hubs for element distribution, as well as the correlation between Cd with Zn/Cu/Co/Mg, between Fe with As.