The invention discloses a sulfur-oxidizing bacterium and a method for removing sulfide by using the sulfur-oxidizing bacterium and belongs to the technical field of biological and environmental protection. The invention discloses the bacterium classified and named Themithiobacillustepidarius JUN-2, and the preservation number is CCTCCNO:M2013217. The bacterium has very high oxidizing efficiency for sulfur compounds, and a byproduct named elemental sulfur with high additional value is efficiently generated. The invention further relates to a method for removing the sulfur compounds in sulfur-containing waste liquid by applying the the sulfur compounds in sulfur-containing waste liquid in a gas lifting type inner circulation continuous operation aerobic reaction device; the hydraulic retention time (HRT) is 10 hours; the yield of the elemental sulfur is 0.1-gL<-1>h<-1>; the generation ratio of the elemental sulfur is about 60 percent; the oxygenation efficiency of thiosulfate is greater than 98 percent. The gas lifting type inner circulation continuous operation aerobic reaction device behaves well, and has a potential to removal of the sulfides in the sulfur-containing waste liquid on large scale.