Upgrading of the anaerobic digestion of waste activated sludge (WAS) by the combination of temperature-phased two-stage digestion and intermediate ozonation was investigated by a continuous experiment with two processes, TM and TOM. The TM process is a temperature-phased two-stage system, which consists of a thermophilic digester and a mesophilic digester in series. The TOM process is a temperature-phased two-stage process with the intermediate ozonation. Two processes were operated at hydraulic retention times of 30 days for over 123 days. Waste activated sludge taken from wastewater treatment plant was fed as a substrate. Microbial community structure in each digester was analysed with molecular tools. Despite of less amount of ozone dose in TOM than ozone pre-treatment process, better effect of ozonation on performance improvement was obtained in TOM. TOM had the highest methane yield and CODCr reduction among comparative processes. Furthermore, flocculation efficiency of TOM followed that of mesophilic digestion. Quality of dewatered supernatant is comparable to mesophilic digestion.