The redox balance of inorganic sulfur in heavily polluted rivers might be disrupted, making sulfur reduction a major metabolic pathway of sulfate-reducing bacteria (SRB), leading to a massive accumulation of S2− and blackening the water bodies. A mixed culture microbial consortium (MCMC) of Citrobacter sp.sp1, Ochrobactrum sp.sp2, and Stenotrophomonas sp.sp3 was used to activate native sulfate-oxidizing bacteria (SOB) to augment the S2− oxidizing process. The results demonstrated that MCMC had a significant sulfur oxidation effect, with 98% S2− removal efficiency within 50 h. The sulfide species varied greatly and were all finally oxidized to SO42−. The mechanism of bio-augmentation was revealed through high throughput sequencing analysis. The MCMC could stimulate and simplify the community structure to cope with the sulfide change. The microorganisms (family level) including Enterococcaceae, Flavobacteriaceae, Comamonadaceae, Methylophilaceae, Caulobacteraceae, Rhodobacteraceae, and Burkholderiaceae were thought to be associated with sulfide metabolism through the significant microbial abundance difference in the bio-treatment group and control group. Further Pearson correlation analysis inferred the functions of different microorganisms: Comamonadaceae, Burkholderiaceae, Alcaligenaceae, Methylophilaceae, and Caulobacteraceae played important roles in S2− oxidization and SO42− accumulation; and Comamonadaceae, Burkholderiaceae, Alcaligenaceae, Methylophilaceae, Caulobacteraceae, Campylobacteraceae, Bacteriovoracaceae, and Rhodobacteraceae promoted the sulfur oxidation during the whole process.