Liuwei Dihuang Pills (LDPs) are a well-known prescription of nourishing yin especially for invigorating kidney-yin. According to the deviation of the structural imbalance of intestinal flora in kidney-yin deficiency patients and the study about polysaccharides having significant added value on intestinal probiotics, it is indicated that there is a possible correlation between intestinal flora metabolism and the mechanism of LDPs intervening in kidney-yin deficiency. In this study, LDPs, a nourishing medicine with rich polysaccharides, are used as the research object. First of all, the kidney-yin deficiency hyperthyroidism rat model was established and evaluated. The appearance of the rats' behavioral, T3, T4, FT3, FT4 and renal histopathology indexes were detected. After LDP treatment for 21 days, the original model of manic rats became more tame and gentle, the T3, T4, FT3 and FT4 values decreased, which gradually approached those contents of the control group rats, and renal pathological sections were shown to be better. Then, we adopted a metabonomics study on urine and excrement of kidney-yin deficiency hyperthyroid rats. 11 metabolites and 18 metabolites were chosen as potential biomarkers among the urine metabonomics study and fecal metabonomics study, respectively. According to the changes of the biomarkers' content, it is speculated that the disorders of metabolism and intestinal flora metabolism occurred after modeling. At the same time, we monitored intestinal flora diversity and metabolic behavior in model rats and LDP-treated rats. Hyperthyroidism caused metabolic disorders of the carboxylic acid cycle, glycometabolism, and amino acid metabolism. Also the energetic metabolism increased the amount of undigested food debris which promoted the growth of the gut microbiome, which may closely relate to the development of the disease. After 21 days of LDP treatment, it was found that LDPs could change the metabolic abnormality, balance structure and quantity of intestinal bacteria, and adjust the diversity of the intestinal flora. The mechanism of LDPs intervening in the metabolism of kidney-yin deficiency hyperthyroidism and the effect of intestinal flora metabolism had a certain connection.