Abstract: To understand the effects of natural fermentation on the changes of phenolic substances in Citrus microcarpa and the inhibition of digestive enzymes, the changes of soluble total phenol, total flavone, α-amylase, α-glucosidase, and pancreatic lipase inhibition rates before and after fermentation were measured. The types of phenolic substances before and after fermentation were identified by UPLC-Q Exactive Orbitrap-MS, and the differential metabolites and their enrichment pathways were screened. Finally, the correlation relationships between the different phenolic metabolites and the inhibitory activities of the above digestion-related enzymes were analyzed based on the correlation coefficient. The results showed that natural fermentation could increase the contents of soluble total phenol and total flavone by 9.20% and 23.68%, respectively, and increase the inhibition rates of α-amylase, α-glucosidase and pancreatic lipase from 11.90% to 28.50%. A total of 52 phenolic substances were detected in Citrus microcarpa. Fermentation did not change the types of phenolic substances, but it significantly increased nine phenolic substances such as nobiletin, caffeic acid, and vitexin, and significantly decreased methoxsarin (P<0.01). The four kinds of pathways significantly affected the change of the above phenolic metabolites, including the biosynthetic pathway of phenylpropane compounds, flavone and flavonol biosynthesis, flavonoid biosynthesis, biosynthesis Ⅰ pathway of various plant secondary metabolites. There was a significant positive correlation between the inhibitory activities of three digestive enzymes and the four different phenolic metabolites, which were nobiletin, apigenin, caffeic acid, and kaempferol (P<0.05). Therefore, natural fermentation can promote the release of soluble total phenol and total flavone in Citrus microcarpa and improve the inhibition rate of digestion-related enzymes, which can be used to effectively process Citrus microcarpa.