Nowadays, heavy metal pollution has become a serious environmental problem on global scale. The heavy metals are non-biodegradable in nature, which can easily accumulate in the organisms of lower trophic level, and enter to the human body system through food chain. Plants, like all other organisms, have evolved different mechanisms to maintain physiological concentrations of essential metal ions and to minimize exposure to non-essential heavy metals. As a first line of defence, many plants exposed to toxic concentrations of metal ions attempt to prevent or reduce uptake into root cells by restricting metal ions to the apoplast, binding them to the cell wall or to cellular exudates, or by inhibiting long distance transport. From this backdrop, the present experiment highlighted the effect of copper (Cu) heavy metals at 0, 0.5, 1.0, 1.5 and 2 mM of copper salt (CuSO4.5H2O) stress (mentioned as Cu stress) in the MS0 medium on Arabidopsis thaliana in terms of growth physiology, metal uptake, biochemistry, and ultra-structural deformation. Ultra structural damage was recorded highest for Cu vascular system at both 1.5 and 2 mM concentration. However, at 2 mM of Cu was the showed highest deformation in root and leaf was observed. Reactive oxygen species (ROS) levels were also higher in plants under stress. Cell wall measurements showed that heavy metal stress has effect on cell wall thickness and also on biomass accumulation. Thus, the first line of defence i.e. cell wall gets affected in the plants when under heavy metal stress.