The effects of Thiobacillus denitrificans combined with signal molecules on the removal of sulfide and nitrate was investigated. By adding signal molecules and T. denitrificans at the same, the total number of microorganisms increased, the removal of sulfide and nitrate was accelerated, and an increase in nitrogen gas and more stable accumulation of elemental sulfur was observed. The total number of microorganisms after the reaction was detected using fluorescence in situ hybridization (FISH) technique. In this experiment, the optimal concentration for the stable accumulation of elemental sulfur from six concentrations of signal molecules was revealed. Further, the effects of adding signal molecules, T. denitrificans, and their combination were analyzed at this concentration. The results showed that it was easier to accumulate elemental sulfur after the addition of 1.0 μmol·L-1 signal molecule. After adding both T. denitrificans and 1.0 μmol·L-1 signal molecules at a sulfide concentration of 200 mg·L-1, the removal of sulfide and nitrate increased to 99.8% and 96.9% at 72 h, respectively, and increases in nitrogen gas and sulfur were observed. The amounts of elemental sulfur and nitrogen gas reached to 59.0 mg and 80.0 mL, respectively, after adding 2.5 μmol·L-1 signal molecules at 72 h when the sulfide concentration was 300 mg·L-1. Under those conditions, the removal efficiency of sulfide and nitrate reached 99.0% and 93.9%, and the production of elemental sulfur and nitrogen reached 63.1 mg and 79.5 mL, respectively.