Autotrophic denitrification process is an effective strategy for treating sulfide and nitrate-enriched wastewater with low organic carbon. This study determined the sulfide oxidation and nitrate reduction rates and characterized the dominant bacteria and microbial community structure stimulated by micro-aerobic conditions in autotrophic denitrification system. With gradually increased sulfide concentration, the sulfide removal rate decreased to 37.8% at S2− = 600 mg/L, while the peak sulfide and nitrate removal rates (100% and 53.8%) were achieved at S2− = 800 mg/L with the air aeration rate of 20 mL/min. The Illumina sequencing results indicated that Thiobacillus accounted for 63% of total operational taxonomic units at generic level with sulfide concentration of 200 mg/L under anaerobic condition. However, Azoarcus, Thauera and Aliidiomorina became the dominant genera under micro-aerobic condition and their abundance significantly and positively related to the sulfide concentration and aeration rate (p < 0.05). According to the 16S metaproteomics functional composition prediction, one potential mechanism for autotrophic denitrifying under micro-aerobic condition was deduced that the oxidation of sulfide to thiosulfate further to sulfite was reinforced by trace oxygen, while the sulfite reductase activity was restrained. The decreased sulfide concentration weakened the toxicity inhibition on denitrifiers and accordingly the performance of autotrophic denitrification process was enhanced by micro-aerobic condition.