Segmentation effect of super accumulation of heavy metals in plants which can reduce the concentration of metal ions in the cytoplasm of a cell is one of the important mechanisms of heavy metal detoxification. However, the compartmentalization effect from different tissues of a cell does not get a consistent conclusion. In order to evaluate whether intracellular compartmentalization could explain Cd detoxification mechanisms, the work described in this paper was designed to study the effect of exposure time and levels on Cd distribution of Indian mustard (Brassica juncea) at the cell and sub-cell level. Root and leaf samples were exposed to 0.5, 1.0, 2.0, 3.0 and 5.0 mg/L and harvested after 1, 5, 7, 10 and 14 days exposure. Cells were separated into three fractions: cytoderm, soluble fraction and organelle containing fraction using differential centrifugation technique, then Cr from all three fractions was determined by Inductively Coupled Plasma-Mass Spectrometry (ICP-MS). Results showed that Cr in cytoderm, cytoplasm and organelles accounted for 50%-64%, 22%-38% and 7%-17% of total cadmium, respectively. It can be clearly indicated that the proportion of Cr in cytoderm is significantly higher than that in cytoplasm and organelles, indicating that compartmentalization of cytoderm plays a prominent role in Cd detoxification. As the exposure concentration and time increases, the content of Cd in cell fraction increases significantly especially after 7 days, which demonstrates that the effect of Cd on plant development is a slow process. Moreover, the excess of Cr stress concentration (  >  1.0 mg/L) would lead to deteriorative damage on plant cells, which was visually identified by TEM research, demonstrating different degrees of damages-plasmolysis, vacuolization and plasmalemma roughness, thus affecting the normal function of cells. These results suggest exposure time and levels are important parameters that must be taken into consideration in the study of the toxicity of heavy metals in plants.