Abstract: To investigate the alternation of fungal microbial community during the storage and maintenance of raw tobacco, the raw tobacco of C3F grade, obtained from and stored in Fujian, Yunnan, and Henan Province consistently or separately, were sampled every 2 months in a year of storage, and high-throughput sequencing was used to analyze fungal community on the surface of raw tobacco. The results showed as the follows. (1) The most abundant species richness and diversity of fungal community occurred in the samples of C3F-2018 from Malong, Yunnan. The fungal community diversity and richness of raw tobacco in different production areas increased at first and then decreased with the extension of storage time, peaking at 6-8 months, and the peaking time was affected by the environment of the storage position. (2) Fungi on the surface of raw tobacco from different production region mainly belonged to four phyla, i.e., Ascomycota, Basidiomycota, Mortierellomycota, and Mucormycota, among which Ascomycota and Basidiomycota were the dominant phyla in the aging process. The numbers of identifiable genera on the surface of raw tobacco from Fujian, Yunnan, and Henan were 19, 22, and 16, respectively, of which the predominant mold belonged to Aspergillus, Xeromyces, Sampaiozyma, Alternaria. This study provide guidance for the mechanism and control of raw tobacco molding.