Three typical biological solid wastes, animal manure, garbage, and sewage sludge, were compared with regard for the composting process and the changes in microbial community structure. The effect of different bulking agents such as rice straw, vermiculite, sawdust, and waste paper were compared in manure compost. The differences in the microbial community were characterized by the quinone profile method. The highest mass reduction was found in garbage composting (56.8%), compared to manure and sludge at 25% and 20.2%, respectively. A quinone content of 305.2 micromol/kg was observed in the late stage of garbage composting, although the diversity index of quinone profile was 9.7, lower than that in manure composting. The predominant quinone species were found to be MK-7, which corresponds to gram positive bacteria with low G+C content such as Bacillus. The predominance of MK-7 was especially found in garbage and sludge composting process, while the increase in quinones with partially saturated long side chain was shown in late composting process of manure, which corresponded to the proliferation of Actinobacteria. The effect of different bulking agents on the composting process was much smaller than the effect of different raw materials. High organic matter content in the raw materials results in a higher microbial biomass and activity, which was connected to the high mass reduction rate.