An alternating mesophilic and thermophilic two stage anaerobic digestion(AD) process was conducted. The temperature of the acidogenic(A) and methanogenic(M) reactors was controlled as follows: System 1(S1) mesophilic A-mesophilic M;(S2) mesophilic A-thermophilic M; and(S3)thermophilic A-mesophilic M. Initially, the AD reactor was acclimatized and inoculated with digester sludge. Food waste was added with the soluble chemical oxygen demand(SCOD) concentrations of41.4–47.0 g/L and volatile fatty acids of 2.0–3.2 g/L. Based on the results, the highest total chemical oxygen demand removal(86.6%) was recorded in S2 while S3 exhibited the highest SCOD removal(96.6%). Comparing S1 with S2, total solids removal increased by 0.5%; S3 on the other hand decreased by 0.1 % as compared to S1. However, volatile solids(VS) removal in S1, S2, and S3was 78.5%, 81.7%, and 79.2%, respectively. S2 also exhibited the highest CH4 content, yield, and production rate of 70.7%, 0.44 L CH4/g VSadded, and 1.23 L CH4/(L·day), respectively. Bacterial community structure revealed that the richness, diversity, evenness, and dominance of S2 were high except for the archaeal community. The terminal restriction fragments dendrogram also revealed that the microbial community of the acidogenic and methanogenic reactors in S2 was distinct. Therefore,S2 was the best among the systems for the operation of two-stage AD of food waste in terms of CH4production, nutrient removal, and microbial community structure.