In order to study the remediation effect of heavily contaminated sediments, the experiments to repair heavily contaminated sediments were carried out under selective and nonselective oxidation conditions. Results showed that a lot of denitrifying bacteria was detected on the surface of modified zeolite by fluorescence in situ hybridization (FISH) after inoculating both nitrifying and denitrifying bacteria for 7 days. Up to 3.69 mg/g, in-situ regeneration of ammonium on zeolite loading with high ammonium (ammonium adsorption: 4.20 m/g) was obtained, which was 1.42 times that of nonselective oxidation (2.60 mg/g). This indicated that the in-situ regeneration rate of zeolite under high ammonium adsorption (5.0 mg/g) and high bacterial inoculum (80 mL/g) was enhanced. Moreover, only 1.50 mg/L total nitrogen with 84% inhibition in the overlying water under selective oxidation conditions was observed, which was 2.37 times the inhibition percentage of modified zeolite under nonselective oxidation conditions. The results illuminated that effective inhibition of ammonium released from heavily contaminated sediments can be achieved through selective oxidation with zeolite layer. At the same time, the in-situ service life of attached biofilm-modified zeolite under selective oxidation conditions was 5.87 years, which was extended by 3 years compared with nonselective oxidation conditions.