The application of anammox process in mainstream wastewater treatment process is still facing challenges especially at the low temperature. To resolve this problem, the coexistence system of anaerobic ammonia-oxidizing bacteria (AnAOB) and heterotrophic bacteria (HB) was built in this study. The nitrogen removal efficiency mainly maintained at above 90% during the process of temperature reducing from 35 °C to 10 °C. The nitrogen removal rate were 0.30 g N·L·d at both 25 and 15 °C and 0.10 g N·L·d at 10 °C, respectively. Analysis of 16S rRNA genus sequencing revealed that as the temperature reduced to 10 °C, the Denutrotisoma genera presented a downward trend but Comamonadaceae genera showed an upward trend. At 10 °C, the contrast of anammox activities between granular and flocculent sludge in the system revealed that although the abundance of anammox genera was much lower in flocculent sludge than that in granular sludge, the anammox activities showed no significant discrepancy. And the abundance of Comamonadaceae and Chloroflexales genera were much higher in flocculent sludge than those in granular sludge, presenting their key roles to anammox activity at low temperature. The Circos diagram and Cluster of orthologous Group of protein functional predication showed that the functional abundance related to interaction among microbial communities were higher in flocculent sludge but those related to self-growth was higher in granular sludge. This result indicated the significance of the interactions based on the microbial diversity in the application of annamox process at low temperature.