The invention relates to the technical field of traditional Chinese medicines, in particular to a gegen-qinlian decoction water extract for regulating an obese body. The gegen-qinlian decoction waterextract is obtained from puerarin, radix scutellariae, coptidis rhizome and radix liquiritiae through medicinal material compatibility and water decoction; the medicinal material compatibility is calculated by the following materials in parts by mass: 7-9 parts of the puerarin, 2-4 parts of the radix scutellariae, 2-4 parts of the coptidis rhizome, and 1-3 parts of the radix liquiritiae; the gegen-qinlian decoction water extract is used for preparing drugs to regulate intestinal flora and liver biological clock genes of intestine damp heat of the obese body, and has the effect of reversing Akkermansia and Lactobacillus, at the same time, the expression and transcription level of liver Clock and Arntl genes is up-regulated, the level of body serum triglyceride can be effectively reduced, and the gegen-qinlian decoction water extract has a regulatory effect on total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, blood glucose, insulin and other blood lipid and blood glucose indexes, and also has a regulatory effect on short chain, medium chain and long chain fatty acids, tryptophan, kynurenine, cannabinoid and other metabolites of the body.