Malachite green from the tri-aryl methane cationic dyes family, despite being toxic, is widely used in many industries. In this study, the removal of malachite green (MG) with Ca-Al-LDH-S2O3 as an adsorbent was studied. Treatment of LDH with thiosulfate ions caused improvement in the interlayer distance of the adsorbent. This adsorbent was synthesized by the co-precipitation method and used to remove malachite green in an aqueous solution. Adsorbent properties were studied using SEM, XRD, BET, FTIR, and DSC techniques. BET surface area for adsorbent was 205.15 m2 g−1. The experimental parameters containing pH = 7.0, adsorbent dose = 0.1 g, initial concentration of pollutant = 100 mg mL−1 and contact time = 120 min were obtained as optimal conditions. Investigation of isotherm models showed that the Freundlich model better fits with the experimental data than the Langmuir model. The maximum capacity at saturation conditions was 909.09 mg g−1. The Pseudo-Second-Order kinetic model was obtained as a dominant kinetic model. The obtained thermodynamic parameters showed that the adsorption process is spontaneous, endothermic and was associated with an increase in system irregularity.