Pollution from concentrated animal feeding operations (CAFOs) are the most serious pollution source in China now, and swine wastewater contains high concentrations of nutrients such as chemical oxygen demand (COD), biochemical oxygen demand 5 (BOD5), ammonium, and emergent contaminants related to public health. Biological processes are the most popular treatment methods for COD and ammonium removal. Considering the low operation cost, easy maintenance and high removal rate of contaminants in recent years, nitrogen removal via nitrite and real-time control processes using oxidation-reduction potential (ORP) and/or pH as parameters to control the aerobic and anaerobic cycles of a system has received much attention for animal wastewater treatment. During the biological treatment process, the emergent contaminants such as estrogen, antibiotics, and disinfec-tion reagents have been the focus of research recently, and degradation bacteria and resistance bacteria have also been extracted from activated sludge. The microbial analysis technique is also advancement in the field of biodegrada-tion bacteria and resistance bacteria. All of these advance-ments in research serve to improve wastewater treatment and decrease environmental hazards, especially for using manure as a fertilizer source for crop production.