Cadmium (Cd) contamination in agricultural soil brings severe health risks through the dietary intake of Cd-polluted crops. The comprehensive role of pectin in lowering Cd accumulation is investigated through low Cd accumulated (L) and high Cd accumulated (H) cultivars of L. sativa. The significantly different Cd contents in the edible parts of two L. sativa cultivars are accomplished by different Cd transportations. The pectin is the dominant responsive cell wall component according to significantly increased uronic acid contents and the differential Cd absorption between unmodified and modified cell wall. The chemical structure characterization revealed the decreased methyl esterification in pectin under Cd treatment compared with control. Significantly brighter LM19 relative fluorescence density and 40.82% decreased methanol in the root pectin of L cultivar under Cd treatment (p < 0.05) supported that the de-methyl esterification of root pectin is more significant in L cultivar than in H cultivar. The pectin de-methyl esterification of L cultivar is achieved by the upregulation of pectin esterases and the downregulation of pectin esterase inhibitors under Cd treatments, which has facilitated the higher Cd-binding of pectin. Our findings provide deep insight into the differential Cd accumulation of L. sativa cultivars and contribute to the understanding the pollutant behaviors in plants.