Periphyton-based bioreactors are widely accepted for removing various pollutants from wastewater; however, the slow start-up and low efficiency in widely fluctuating temperatures limit its application. A spiral periphyton bioreactor (SPR) was developed and its COD removal capability and the associated microbial communities were investigated. This SPR can be easily backwashed to stimulate periphyton growth and efficiently remove COD at temperatures ranging from 4 to 30 °C. The species richness and evenness of the periphyton community increased during domestication, while its functional diversity and organic carbon metabolic vitality were higher after 30 days domestication. Cyanobacteria were the main components of the SPR and produced an aerobic environment, while Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Sphingobacteria were the microorganisms responsible for COD removal. This study provides valuable insights into changes in pivotal microorganisms of the periphyton community during domestication, and indicates that SPR is simple to operate and efficient in COD removal.