To understand the effect of microbial community on the flavor of fermented rice wine, microbiomes in three traditional starters (CMQ, NBQ, and YCQ) from different origins for making Chinese rice wines were evaluated and the volatile components of their rice wines were compared. The results showed that the dominant genera in CMQ were Pantoea, Bacillus, Rhizopus, and Candida, the dominant microorganisms in NBQ were Pediococcus, Lactobacillus, Acetobacter, Weissella, Bacillus, Rhizopus, Candida, and Aspergillus, the dominant microorganisms in YCQ were Pediococcus, Lactobacillus, Leuconostoc, Weissella, Lactococcus, Ochrobactrum, Rhizopus, and Mucor. There were significant differences in sensory properties of the wines brewed by three starters. Although the major aroma components were benzyl alcohol, 2-octanone, benzoic acid, and phenethyl acetate, each rice wine had its own main aroma components include 1-octanol, 1-pentanol, ethyl acetate, etc. The results showed that the different microbial communities in starter results in the significant difference of the aroma components in its fermented rice wine.