In order to study the method of sediment resource utilization in the malodorous river, and to evaluate the nutrient removal efficiency using modified sediment and its removal mechanism, the sediment samples (S) from a seriously malodorous river in Beijing were collected in this study. The sediment was modified by oxidation and metal ion-loaded (MS). The nutrient removal efficiency for S and MS was evaluated. The removal mechanism of nutrient was studied through kinetics, equilibrium, and thermodynamic experiments. The results indicated that when the environmental temperature was 35℃, and solid to liquid ratio was 1:50 (g:ml), the nitrogen (initial concentration, 20 mg/L) and phosphorus (initial concentration, 10 mg/L) removal efficiency by using MS was up to 90% and 98%, respectively. The pseudo-second-order model could better describe the sorption kinetics (R²>0.93), and the kinetic and isotherm study illustrated that data from the isotherm experiments were well described by Langmuir isotherm model. The sorption capacity reached 0.891 mg/g for nitrogen and 0.474 mg/g for phosphorus, respectively. The thermodynamic result suggested that enthalpy (ΔH⁰) and entropy (ΔS⁰) were positive, and Gibbs energy (ΔG⁰) was negative during the adsorption experiments. The values of ΔG⁰ decreased with the increase of temperature. The results showed that MS had the higher nutrient sorption capacity, and the exterior activated site had the main function of phosphorus and nitrogen sorption. The sorption process was a spontaneous or endothermic reaction, and high temperature was in favour of sorption. In addition, the results also indicated that desorption occurred more easily than sorption at the same temperature.