In the present study, ectopic fermentation systems were treated with both solid and liquid waste from livestock. Then, the various physicochemical properties and compositions of microbial communities in different waste straws treatments were compared. The addition of thermophilic bacteria was beneficial to the decomposition of litter, and it improved the fermentation process. Proteobacteria, Bacteroidetes, and Firmicutes were the predominant types in the fermentation vessels, and the presence of the phyla Proteobacteria and Bacteroidetes was correlated with factors prevailing in the mature phase. Furthermore, pig manure with sawdust, rape stem, and rice chaff and pig manure with sawdust, rice straw, and rice chaff vessels had higher concentrations of dissolved nitrogen, which were conducive to the conversion of fermentation wastes into useful fertilizer. These results demonstrate the feasibility of using rape stem and rice straw as padding materials during the treatment of both liquid and solid livestock waste in ectopic fermentation systems.