The invention discloses a compound microbial active filling material for removing sulphur-containing repugnant substances, as well as preparation and application of the compound microbial active filling material. Ochrobactrum anthropi SL1 and aquamicrobium defluvii SU1 related in the invention are isolated bacteria obtained in a reactor for processing repugnant substances, such as H2S, in a water pollution control laboratory of the ecological environment research centre of the Chinese academy of sciences. The bacterial strains are preserved in the general microbial centre of the Chinese general microbial strain preservation and management committee. The preservation numbers are CGMCC No.7400 and CGMCC No.7399 respectively. The compound microbial active filling material disclosed by the invention has the advantages of being large in specific area, high in porosity, good in air permeability, low in resistance, high in bacterial cell loading capacity and less prone to run away; and because of being loaded with ochrobactrum anthropi SL1 and aquamicrobium defluvii SU1, the compound microbial active filling material is difficult to decay and deform in a bioreactor for purifying waste gas, and therefore, the compound microbial active filling material can be used for a long time and is applied to complex processing conditions.