The reactivation and granulation processes of damaged anaerobic microbial communities were studied. The changes of population structure of several typical functional microbes like E. limosum (E-HOMA), Methanomicrobiales (M-methanogens), Syntrophics fatty acid - β - oxidizing syntrophic bacteria and Syntrophic propionate - oxidizing bacteria (FP-HPA) were investigated. The results showed that the maximum abundance of bacteria and archaea was observed only through 33 days continuous incubation, much less than the time needed for sludge granular size increase (>180 days) and for achieving good COD removal (about 50 days). In comparison with FP-HPA and E-HOMA, the M-methanogens had stronger resistance for poor living conditions and enriched more quickly with environment improvement. During sludge granulation, the growth rate of microbial species was ranked in the order of M-methanogens > FP-HPA > E-HOMA. Compared with the initial microbial abundance of seed sludge, the initial microbial diversity may play more important role during sludge granulation. The reactivation of damaged microbial communities during sludge granulation was composed by three distinct periods, namely adaptation period, growth period and stable period.