Given the disadvantages of the traditional “water-driven sediment” restoration technology, which is easy to return to black and odorous for the treated sediment, a novel treatment mode of “treating sediment before water” was proposed. Based on the idea of “sustained-release functional materials in coordination with microbial denitrification enhancement to drive the removal of oxygen-consuming substances from sediment”, a synchronous removal technology of carbon, nitrogen and sulfur pollutants from sediment was developed and was demonstrated in the pilot application. The results showed that, after 60 days of in-situ remediation, the removal efficiencies of TOC, TN and AVS in the sediment were 36% to 41%, 45% to 58%, and 89% to 91%, respectively, and the oxidation layer depth in sediment reached 15.5 to 17.6 cm. This new model and new technology can effectively oxidize deep sediment to improves the water quality, protecting the river environment health.