Based on the highthroughput DNA sequencing of Illumina, the microbial community composition of the compost of rice straw added with urea or cow dung as the nitrogen source was entirely clarified, respectively. Totally 897 and 954 bacterial operational taxonomic unit (OTU) was obtained from the treatment applied with urea and manure, targeting the V4 region of bacterial 16S rRNA partial gene. The richness index and diversity index of bacterial community in the treatment applied with manure were higher than that in the treatment applied with urea. In the treatment applied with urea, the bacterial phylum Actinobacteria was the most dominant group (71.9%), and the genus Streptomyces and Cellulosimicrobium were the main genus of 40.9% and 22.2%, respectively. In the treatment applied with manure, the bacterial phylum Proteobacteria was the most dominant group (58.5%), and the genus Pseudomonas was the main genus of 47.8%. Totally 508 and 585 eukaryotic microbial operational taxonomic unit (OTU) was obtained from the treatment applied with urea and manure, targeting the V4 region of eukaryotic 18S rRNA partial gene. The richness index and diversity index of eukaryotic community in the treatment applied with manure were higher than that in the treatment applied with urea. In the treatment applied with urea, the fungal phylum Ascomycota was the most dominant group (70.0%), and the genus Pichia was the main genus of 46.1%. In the treatment applied with manure, the fungal phylum Ascomycota was still the most dominant group (42.5%), following by the fungal phylum Zygomycota (20.5%). The genus Aspergillus (23.9%) and Mucor (9.4%) were the main genus. The results showed that different nitrogen sources could lead to the formation of bacterial and eukaryotic microbial communities with different predominant population structures in crude fertilizers from rice straw compost fermentation, which may lead to the differences of microbial groups that played a role in the stages of composting. Isolation and compounding of the above dominant microbial populations, together with the application of appropriate urea and manure, was likely to make the process of fermenting rice straw to crude fertilizers more rapid.