Honeys produced from medicinal plants hold great promise for human health. Herein, we determined the chemical composition and gastrointestinal protective effects of a novel monofloral honey from Prunella vulgaris (PVH). The physicochemical parameters (moisture, sugars, pH, protein content, diastase activity, and hydroxymethylfurfural) of the PVH samples met the criteria specified in European Union regulations and Chinese National Standards. Fifteen phenolic compounds were identified and quantified via high-performance liquid chromatography with a diode array detector and with time of flight tandem mass spectrometry detection (HPLC-DAD/Q-TOF-MS). Rosmarinic acid was found to be a potential marker for PVH identification. Using a dextran sulfate sodium (DSS)-induced acute colitis model, we demonstrated that the administration of PVH (5 g per kg b.w., p.o.) significantly decreased the disease activity index and mitigated colonic histopathological changes in rats. PVH also modulated the gut microbiota composition in the colitic rats, reversing the increase in the Bacteroidetes/Firmicutes ratio and restoring Lactobacillus spp. populations in DSS-challenged rats. The results of this study provide fundamental data on PVH, supporting its future application in the prevention of colitis.