Objective To explore the synergistic therapeutic effect of sodium butyrate and Sishen pill on mice with diarrhea with kidney-yang deficiency syndrome, and provide experimental evidence for the contemporary application of classical prescriptions. Methods The diarrhea with kidney-yang deficiency syndrome mouse model was constructed by gavage of adenine combined with Folium sennae. Mice were given 100% Sishen pill decoction, 50 mg/kg sodium butyrate+75% Sishen pill decoction, 100 mg/kg sodium butyrate+50% Sishen pill decoction, 200 mg/kg sodium butyrate+25% Sishen pill decoction, and 300 mg/mL sodium butyrate decoction by intragastric administration, respectively. General condition, food and water intake, anal temperature, body weight, fecal water content, organ index, intestinal microbiota, and enzyme activity of the mice were compared. Results After treatment, the general condition, food and water intake, anal temperature, and fecal water content of the mice gradually recovered. The body weight of mice from the natural recovery group, the 200 mg/kg sodium butyrate+25% Sishen pill group, and the 50 mg/kg sodium butyrate+75% Sishen pill group still showed statistical differences from the normal group (P<0.05). The body weight of mice from the 100 mg/kg sodium butyrate+50% Sishen pill group (34.23±4.93) g increased, close to the body weight of mice from the normal group (35.69±4.78) g. Spleen index of the mice from the 100 mg/kg sodium butyrate+50% Sishen pill group recovered to normal, showing significant difference from mice from the natural recovery group (P<0.05). There were no significant differences in thymus index of mice from different groups (P>0.05). After treatment, the mice intestinal microbiota began to recover, with no significant differences in the number of bacteria among groups (P>0.05). Compared with the natural recovery group, the number of Escherichia coli in mice from each treatment group reduced significantly (P<0.01), and the mice from 100 mg/kg sodium butyrate+50% Sishen pill group had the smallest number of Escherichia coli. The number of Bifidobacteria in mice from the 100 mg/kg sodium butyrate+50% Sishen pill group and the 50 mg/kg sodium butyrate+75% Sishen pill group recovered to the level of the normal group (P>0.05). The mice from 100 mg/kg sodium butyrate+50% Sishen pill group showed a significant effect on the recovery of Lactobacillus number (P<0.05). The amylase, lactase, and protease activities in mice from the natural recovery group were all higher than those from the normal group (all P<0.05), and the enzyme activities in mice from the 100 mg/kg sodium butyrate+50% Sishen pill group were closer to those from the normal group. Compared with the natural recovery group, lactase activity of mice from the 100% Sishen pill group reduced significantly (P<0.01), and the xylanase activity in mice from the 100 mg/kg sodium butyrate+50% Sishen pill group was closest to the normal group. Conclusion The synergistic effect of sodium butyrate enhances the therapeutic efficacy of Sishen pill. 100 mg/kg sodium butyrate+50% Sishen pill group showed significant improvement in mice mental status, diarrhea symptoms, intestinal enzyme activity, and microbial stability compared with other groups using sodium butyrate or Sishen pill alone.