The increased pollution of water resources by toxic heavy metals poses a huge threat to the aqueous ecosystem. Since the low concentrations of heavy metals are often highly toxic but difficult to remove, novel efficient adsorbents still need to be explored. Herein, the superparamagnetic thiol-functionalized oxygenous carbon nitride nanocomposite (CNO/Fe3O4-SH) with multifunctional groups such as –NH2, –OH, –SH, and –COOH was fabricated by a simple and eco-friendly method. The maximum adsorption capacities of Pb2+, As3+, and Cd2+ ions on CNO/Fe3O4-SH at pH = 6 were 80.79, 71.78 and 66.19 mg/g, respectively, when their equilibrium concentrations were 20 mg/L. Under the equilibrium concentration below 0.01 mg/L, the adsorption capacities of these heavy metals over CNO/Fe3O4-SH were much higher than those of other adsorbents. The competitive adsorption investigations showed that the adsorption order in polymetallic solutions was Pb2+ > As3+ > Cd2+. Adsorption kinetics and isotherms studies indicated that the adsorption of Pb2+, As3+ and Cd2+ by CNO/Fe3O4-SH was attributed to monolayer adsorption and the adsorption process was controlled by chemical adsorption. The thermodynamic experiments showed that the adsorption processes were spontaneous and endothermic. After six adsorption/desorption cycles, CNO/Fe3O4-SH maintained its original morphology and adsorption ability, indicating its excellent regeneration performance, which had significant potential application in the decontamination of trace heavy metal ions in water.