Metabolic syndrome caused obesity has long been recognized as a risk of health. Celery and celery extracts have various medicinal properties, such as anti-diabetes and anti-inflammatory properties and blood glucose and serum lipid reduction. However, the effect of probiotic fermentation on celery juice and the association between fermented celery juice (FCJ) and obesity were unclear. This study aimed to evaluate the beneficial effects of FCJ on high-fat diet (HFD) induced obesity and related metabolic syndromes. C57BL/6 mice were randomly divided into six groups (n = 15 per group) fed either a normal diet (ND) or HFD with or without CJ/FCJ (10 g kg-1 day-1) by oral gavage for 12 weeks. Here we demonstrated that the probiotic fermentation of celery juice (CJ) could enhance the active ingredients in celery, such as total polyphenols, flavonoids, vitamin C and SOD. Compared to the slight improvement induced by CJ ingestion, FCJ intake significantly inhibited body weight gain, prevented dyslipidemia and hyperglycemia, and suppressed visceral fat accumulation. Furthermore, 16S rRNA sequencing analysis revealed that FCJ intake altered the composition of gut microbiota, increasing the ratio of Firmicutes/Bacteroidetes and the relative abundance of beneficial bacteria (Lactobacillus, Ruminococcaceae_UCG-014, Faecalibaculum and Blautia), and decreasing the relative abundance of harmful bacteria (Alloprevotella and Helicobacter). These findings suggest that FCJ can prevent HFD-induced obesity and become a novel gut microbiota modulator to prevent HFD-induced gut dysbiosis and obesity-related metabolic disorders.