The use of Bacillus circulans as the sole starter provides better process control compared to natural fermentation. However, the chemical composition of fermented Tibetan tea by B. circulans and its regulatory effects on the intestine–liver axis has not been reported. For this purpose, a high-resolution liquid chromatography tandem mass spectrometry metabolomics approach was performed. The effects of fermented Tibetan tea on the intestine–liver axis of mice were also evaluated. Untargeted metabolomics analysis showed that the contents of catechin derivatives, flavonoids, phenolic acids, and terpenoids increased by 0.3, 2.38, 2.65, and 3.36%, respectively, compared with those before fermentation. Furthermore, 16S ribosomal RNA sequence analysis revealed that the relative abundance of Lactobacillus spp. in the intestine increased after consumption of fermented tea. Additionally, based on histological and quantitative PCR analyses, fermented Tibetan tea also improved intestinal development and intestinal barrier function in mouse, while increasing the antioxidant capacity of mouse liver. Thus, fermented Tibetan tea could provide beneficial health effects through the intestine–liver axis. These findings have facilitated the study of the chemical composition of Tibetan tea and provided theoretical support for its use as a natural beverage with intestinal probiotic functions.