Autotrophic nitrogen removal technology is a key component to achieve the energy recovery from wastewater, with characteristics of low aeration intensity and low organic carbon requirements. However, functional microbial communities in the autotrophic nitrogen removal process including ammonia oxidizing bacteria, nitrite oxidizing bacteria, and anaerobic ammonia oxidization bacteria are all slow growing microorganisms, preferring to grow in the form of granules or biofilms. In addition, all these microorganisms have to work together to complete autotrophic nitrogen removal. Therefore, microbial interactions among possible functional microorganisms are important aspects that should be clarified so as to advance the autotrophic nitrogen removal process. The density dependent growth and the microbial community interaction characteristics indicate that quorum sensing should play an important role in this process. Previous studies confirmed the production of signal substances responsible for quorum sensing by autotrophic nitrogen removal microorganisms. In addition, the dosage of external signal substances could promote microbial activity, and also enhance the biofilm growth or extracellular polymeric substances production. In the autotrophic nitrogen removal processes, microbial interactions include nitrogen cycle, carbon cycle, and cross talk among microbial communities, which should be focused on in future studies.