Rose jam is a traditional fermented food in China, fresh rose petals and sugar are the main materials. It is thoroughly rubbed and fermented at room temperature for about a month. The purpose of this study was to explore the dynamic changes of microorganisms, physicochemical properties and flavor compounds in rose jam during fermentation. High-throughput sequencing and headspace-gas chromatography-ion mobility spectroscopy (HS-GC-IMS) were used to study the microbial diversity and volatile compounds in the fermentation of rose jam. The dominant bacterial genera were Streptophyta, Pantoea and Rosenbergiella, and the dominant fungi were Alternaria, Podosphaera and Botryotinia. Rose jam contains rich bioactive compounds, especially anthocyanins, polyphenols and flavonoids. The content of benzene acetaldehyde, benzaldehyde, 2-methylbutanal, hexanal, exenol and n-hexanol in rose jam decreased gradually with the fermentation time. At the same time, the contents of some aldehydes (furfural, pentanal, heptanal and 3-methylbutanal), alcohols (2-methyl-1-propanol, 3-methylbutanol-1-ol, 2-methylbutanol-1-ol, heptanol and pentane-1-ol) and ketones (methyl-5-heptan-2-one and 2,3-butanedione) gradually increased with the extension of fermentation time. These results will help the production mechanism of rose jam fermentation process, and further strengthen the quality control of rose jam, and promote standardized production.