Objective: To explore the physiological regulatory mechanisms of Bifidobacterium triple bacteria (probiotics) on the infectious diarrhea newborn. Methods: 130 cases of infectious diarrhea newborn in our hospital from February 2013 to February 2015 were selected as the study objects, and randomly divided into the control group and treatment group, 65 cases in each group. The control group were given conventional treatment, and the treatment group were given probiotics therapy. The physiological regulatory mechanisms on newborn were compared and analyzed. Results: In the study, the total treatment effective rate in the control group was 69.2%, and treatment group 89.2%, showing that the effect in the treatment group was significantly better than that in the control group (P<0.05). There were 10 cases occurring adverse reactions in the control group, with adverse reactions incidence of 15.4%, and 3 cases in the treatment group, with adverse reactions incidence of 4.6%, the difference was significant (P<0.05). The disappeared time of diarrhea, vomiting, fever and other adverse symptoms in the treatment group were significantly shorter than that in the control group, with significant differences (P<0.05). Conclusion: The adjuvant therapy of probiotics on infectious diarrhea newborn has significant clinical regulatory value. This therapy can effectively reduce the clinical adverse reactions and is worthy of clinical promotion and applications.