Human intestinal microbiota comprise a complex biological system with considerable metabolic activity. Various studies have focused on the bioconversion of flavonoids. However, in addition to flavonoids, bioactive components such as iridoids also exist in many natural and traditional Chinese medicines. Little is known about the interactions of the iridoids with bacteria. Loganin, one of the main effective iridoids in the valuable traditional Chinese herbal medicine Cornus officinalis, exhibits various pharmacological activities and biological effects. Human intestinal bacteria were isolated and the conversion capability of loganin was investigated. The metabolites were determined by ultra-high performance liquid chromatography–quadrupole time-of-flight mass spectrometry. Loganin was metabolized to hydrogenated and hydroxylated loganin sulfate, acetylated loganin, loganetin, methylated loganetin, hydrogenated, and hydroxylated loganetin. The metabolic routes and metabolites of loganin were reported for the first time. These metabolites may influence the biological activities of loganin in vivo. Thus, this study provides fundamental information about a traditional Chinese medicine.