This paper aimed at developing the enhanced biological treatment processes for treating avermectin fermentation wastewater (AFW). After UASB treatment and chemical coagulation, the pretreated AFW was subsequently flowed into a rCAA reactor (reactor with repeated coupling of aerobes and anaerobes using macroporous carriers) system for further pollutant degradation and excess sludge reduction. By the treatment with chemical coagulation, COD, total nitrogen and total phosphorus concentration of treated AFW were eliminated to 550–700 mg/L, 130–160 mg/L and 1 mg/L, respectively, and the dark color of the wastewater was greatly bleached. After this decolorized wastewater was treated by the following rCAA bioreactor, the COD could be reduced to around 200–300 mg/L, while the further decrease of COD less than 200 mg/L was difficult. The Biolog analysis and OUR test for the water treated by rCAA bioreactor demonstrated that the effluent from chemical coagulation contained some unknown compounds with low biodegradability and would simplify the microbial community in the subsequent rCAA reactor.