An acidogenic reactor with a 0.5-L working volume and a methanogenic digester with a 5-L of working volume were operated for 150 days on a continuous mode to investigate the structure of a microbial community during food wastewater treatment. During the steady state of anaerobic digestion, volatile solids (VS) removal efficiency in the pilot plant was approximately 65%. The bacterial population was higher than any other methanogens detected during the entire anaerobic process and treatment of raw food wastewater. Methanomicrobiales (MMB), Methanosarcinales (MSL), and Methanobacteriales (MBT) were detected during digestion. The methanogenic population present in the acidogenic reactor was directly affected by the archaeal community in raw food wastewater. However, the shift of microbial community in the methanogenic digester was relatively gradual. The performance of methanogenic digester might be more related to the change of microbial metabolism affected by the physicochemical properties of the input substrate.