Ulcerative colitis (UC) often occurs accompanied by colonic leakage and flora imbalance, resulting in secondary liver injury (SLI). SLI, in turn, aggravates UC, so the treatment of UC should not ignore it. beta-patchoulene (beta-PAE), a tricyclic sesquiterpene isolated from Pogostemon cablin, has been reported to exert a protective effect in gastrointestinal disease in our previous studies. However, its protection against UC and SLI remains unknown. Here we explored the protective effect and underlying mechanism of beta-PAE against dextran sulfate sodium induced UC and SLI in mice. The results indicated that beta-PAE significantly reduced disease activity index, splenic index and attenuated the shortening of colonic length in UC mice. It alleviated colonic pathological changes and apoptosis through protecting tight junctions, reducing neutrophil aggregation, and inhibiting the release of pro-inflammatory cytokines and adhesion molecules. These effects of beta-PAE were associated with the inhibition of TLR4/MyD88/NF-kappa B and ROCK1/MLC2 signalling pathway. UC-induced colonic leakage caused abnormally high LPS levels to result in SLI, and beta-PAE markedly inhibited it. beta-PAE simultaneously ameliorated SLI with reduced biomarker levels of endotoxin exposure and hepatic inflammation. High levels of LPS were also associated with flora imbalance in UC mice. However, beta-PAE restored the diversity of gut microbiota and altered the relative abundance of characteristic flora of UC mice. Escherichia-dominated gut microbiota of UC mice was changed to Oscillospira-dominated after beta-PAE treatment. In conclusion, pharmacological effects of beta-PAE on UC and SLI were mainly contributed by suppressing colonic leakage and flora imbalance. The findings may have implications for UC treatment that not neglect the treatment of SLI.