In this work, a novel organic–inorganic hybrid-based Fe3O4 nanoparticles was developed to remove metal ion and organic contaminants from aqueous solutions with the most serious environmental problems. In order to remove pollutants including Mercury(II) chloride (HgCl2), Alpha lipoid acid (ALA), Methyl orange (MO), Fe3O4@SiO2@APTS functionalized oxidized chitosan (Fe3O4@SiO2@APTS-OCS) was synthesized, and these composites were characterized by FT-IR, XRD, FE-SEM, VSM and BET techniques. In addition, a simple and fast multi-stage heating method was provided to produce mercury chloride under a closed laboratory system. The purification of mercury (II) chloride showed > 99.99%. Then, Hg2+, ALA and MO removal can be carried out by Fe3O4@SiO2@APTS-OCS with the optimum equilibrium conditions. The adsorbent catalyst dosage Fe3O4@SiO2@APTS-OCS was obtained 0.35 g/L. The initial concentration parameter for Hg2+, ALA and MO removal was calculated 30 mg/L. In addition, optimum initial pH value for Hg2+, ALA and MO removal was obtained 11, 1 and 1, respectively. After six consecutive cycles, Hg2+, ALA and MO adsorption by nano-composite were decreased from 89.0 to 78.0%, 85.0 to 76.0%, and 92 to 79, respectively. The quantum and molecular dynamic calculations were studied to obtain optimization of structures and removal of Hg2+, ALA and MO by Fe3O4@SiO2@APTS-OCS in Materials Studio 2017 software. Based on the negative adsorption energy (ΔEads) of Hg2+, ALA and MO on nanoparticles, the simulation system was the stability and placed spontaneously in parallel above Fe3O4@SiO2@APTS-OCS by forming hydrogen bonds and van der Waals. [ABSTRACT FROM AUTHOR]