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Chinese rice wine (Huangjiu) has a long history and has been popular in China for thousands of years. During Huangjiu fermentation, many kinds of microorganisms are involved and hundreds of metabolites are produced, which form its unique aroma. The composition of the Huangjiu microbiome has a strong influence on the flavor and quality of the final consumer product. Therefore, this review summarizes the research progress on the main components, quality control indicators and flavor compounds, as well as potential hazards during the fermentation of Huangjiu. The influence of the dominant microbial species on the Huangjiu fermentation, the sensory qualities and the formation of harmful substances are discussed. This helps to provide a theoretical basis for modification of the Huangjiu microbiome to improve control of the fermentation process and the overall sensory quality of the final product.