Aims <p>Pectin plays an important role in cell wall cadmium (Cd) immobilization. The molecular structure of pectin exerts a pronounced influence on its immobilization ability. This study investigates the structural modifications of pectin in root and leaf cell walls of hyperaccumulators under Cd stress and explores the mechanisms underlying Cd immobilization.</p> Methods <p>Two kinds of Cd concentrations (50 and 100&#xa0;μM) were set up in this experiment to study the physiological reactions of pectin and the structural changes of pectin polysaccharides in the root and leaf cell walls of <i>Solanum nigrum L</i>.</p> Results <p>According to the results of Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectrometer (XPS), Cd stress can induce numerous free hydroxyl and carboxyl groups in pectin. These hydroxyl and carboxyl groups may be derived from the modifications of Pectinase (PG) and pectin methylesterase (PME), and may be the main sites for the immobilization of Cd in pectin. Moreover, the structure of pectin was characterized. With the increase of Cd stress, both the proportion of homogalacturonan (HG) and the linearity of pectin increased. Increased HG could enhance the immobilization of Cd through structures such as "egg-box", indicating that structural changes also play an important role in the immobilization of Cd by pectin.</p> Conclusions <p>In the range of 0–100&#xa0;μM Cd, pectin in leaves tended to immobilize Cd by increasing the proportion of HG components and the linearity of pectin. In roots, variations in PME enzyme activity and HG components also affect the immobilization of Cd by pectin.</p>