The study aims to observe the clinical efficacy of Baoerkang san on spleen-deficiency and dampness-obstructing diarrhea in children. Children diarrhea divided into acute diarrhea (group I) and chronic persistent diarrhea (group II). A randomized, double-blind, positive control test was conducted for dose finding. The 340 cases with acute diarrhea in group I were divided into three groups: the high dose group (112 patients), the low dose group (113 patients) and the positive control group (115 patients), which were treated for 3 days. Their clinical efficacies were compared to evaluate the clinical safety of Baoerkang san. The 167 patients with chronic persistent diarrhea in group If were divided into the high dose group (56 patients), the low dose group (55 patients) and the control group (56 patients), which were treated for 5 days. Their clinical efficacy were compared to evaluate the clinical safety of Baoerkang san. According to the results, the cure rate and the effective rate of acute diarrhea and chronic persistent diarrhea in the high dose group and the low dose group were significantly higher than that of the positive control group (P <0. 05, P < 0.01). In the treatment of spleen-deficiency and dampness-obstructing diarrhea with traditional Chinese medicines, the cure rate and the effective rate of acute diarrhea and chronic persistent diarrhea in the high dose group and the low dose group were significantly higher than that of the positive control group (P < 0.05, P < 0.01). During the test, all of the three groups did not suffer any adverse event, with no any abnormality in general physical indexes. In conclusion, Baoerkang san shows a significant efficacy in treating acute diarrhea and chronic persistent diarrhea (spleen-deficiency and dampness-obstructing) and safe clinical application.