To explore the relationship between process stability and microbial community in anaerobic digestion, organic loading rate (OLR) disturbances were introduced into an anaerobic digester treating food waste (FW) to induce different process stages. Physico-chemical analysis along with the 454-pyrosequencing microbial technique were performed to monitor the responses of state parameters as well as the dynamics of microbial community. Results showed that balanced community structure ensured the stable operation of the digester. Under steady-state conditions, the methane yield reached (0.50±0.01) LCH₄/gVS and volatile solids (VS) removal rate reached (89.58±0.08)%. Under high OLR conditions, the relative abundance of acid-producing bacteria (phyla Tenericutes and Actinobacteria) increased dramatically, which induced the proliferation of syntrophic fatty acid degrading bacteria (class Clostridia), while the abundance and activity of syntrophic hydrogenotrophic methanogens decreased. The imbalance relationship between methanogens and syntrophic fatty acid degrading bacteria caused their inefficient syntrophy, eventually resulting in volatile fatty acid (VFA) accumulation and process deterioration. Moreover, the accumulated VFA and ammonia reduced the specific acetoclastic methanogenic activity (SAMA) and specific methanogenic activity (SMA) by 60.12% and 72.51%, respectively, which further deteriorated the digestion process. Although the digester afterwards recovered to its original operational conditions and process performance, the microbial community profile changed and achieved new steady-state conditions.