This study synthesized a new thiomalic acid–modified rice husk biochar (TMA-BC) as a versatile and eco-friendly sorbent. After undergoing chemical treatments, the mercerized rice husk biochar (NaOH-BC) and TMA-BC samples showed higher BET surface area values of 277.1 m²/g and 305.8 m²/g, respectively, compared to the pristine biochar (BC) sample, which had a surface area of 234.2 m²/g. In batch adsorption experiments, it was found that the highest removal efficiency for malachite green (MG) was achieved with TMA-BC, reaching 96.4%, while NaOH-BC and BC exhibited removal efficiencies of 38.6% and 27.9%, respectively, at pH 8. The engineered TMA-BC exhibited a super adsorption capacity of 104.17 mg/g for MG dye at pH 8.0 and 25 °C with a dosage of 2 g/L. The SEM, TEM, XPS, and FTIR spectroscopy analyses were performed to examine mesoporous features and successful TMA-BC carboxylic and thiol functional groups grafting on biochar. Electrostatic forces, such as π − π interactions, hydrogen bonding, and pore intrusion, were identified as key factors in the sorption of MG dye. As compared to single-solution adsorption experiments, the binary solution experiments performed at optimized dosages of undesired ions, such as humic acid, sodium dodecyl sulfate surfactant, NaCl, and NaSCN, reflected an increase in MG dye removal of 2.8%, 8.7%, 5.4%, and 12.7%, respectively, which was attributed to unique mesoporous features and grafted functional groups of TMA-BC. Furthermore, the TMA-BC showed promising reusability up to three cycles. Our study indicates that mediocre biochar modified with TMA can provide an eco-friendly and cost-effective alternative to commercially accessible adsorbents.