In this study, we investigated the effects of dark tea with Pericarpium Citri Reticulatae on body mass growth (BMG), fasting serum glucose (FSG), glucose tolerance (GT), serum insulin, serum lipids and gut microbiota in C57BL/6J mice with metabolic disorders induced by a high-fat diet. Our data showed that intervention with the tea at a dose of 0.75–3.00 g/kg m_b lowered FSG in the mouse model of metabolic disorders. The intervention at 3.00 g/kg m_b improved GT and ameliorated early hepatic fat deposition. Hepatic total cholesterol was decreased significantly in the middle-dose (1.50 g/kg m_b) intervention group. Moreover, consumption of the dark tea reversed the change in gut microbiota relative abundance induced by the high-fat diet and decreased the relative abundance of Proteobacteria and the ratio of Firmicutes/Bacteroidetes. At the genus level, the dark tea inhibited the relative abundance of Desulfovibrio, Lactobacillus and Lactococcus but increased the abundance of Clostridium and Lachnospiraceae_NK4A136_group. Metabolic pathway analysis revealed that lactate dehydrogenase and 6-phospho-β-glucosidase, key enzymes of glycolysis, were down-regulated, resulting in inhibition of the synthesis of lipoteichoic acid associated with the enrichment and adhesion of Gram-positive bacteria. Based on these findings, we speculated that dark tea with Pericarpium Citri Reticulatae may protect the intestinal epithelial barrier and regulate fatty acid absorption, bile acid metabolism and lipolysis, thereby ameliorating glucose metabolism and liver fat deposition. Thus, this tea is expected to be a potential healthy beverage regulating the gut microbiota and improving glucose and lipid metabolism.