Fast food is becoming increasing popular as a social phenomenon, and it usually contains high fat contents. Matcha is one versatile tea, and its application in food brings lots of new consumers. Herein, a high-fat diet containing matcha was prepared, and in this study we investigated the effects of such a diet on lipid metabolism and intestinal flora of normal and diabetic mice. Results showed that diabetes had significant weight loss, hyperphagia, hyperlipidemia and intestinal flora disturbance, with particularly significantly increased Alistipes, Prevotella, Helicobacter, Acetatifactor and Bacteroides, and decreased Alloprevotella, Lactobacillus, Allobaculum and Akkermansia. In diabetes, matcha decreased serum triglyceride and LDL-C, increased HDL-C, reversed those bacteria trends besides Alistipes, Prevotella and Akkermansia. In normal mice, matcha decreased serum LDL-C, increased Parabacteroides, Bacteroidales_unclassified, Erysipelotrichaceae_unclassified and Barnesiella, Lachnospiraceae_unclassified, and decreased Helicobacter and Clostridium XlVa. Most importantly, matcha increased Porphyromonadaceae_unclassified, Lactobacillus, Alloprevotella, Prevotella and Allobaculum; and decreased Bacteroides and Enterobacteriaceae_unclassified in diabetes, however these changed bacteria in normal mice showed an opposite trend from diabetes. Intestinal flora balance is vital important to host, matcha helps to improve the balance of lipid metabolism and intestinal flora according to different character of host, and is a valuable addition to develop functional food.