Background Enterocolitis (EC) is the most common and serious postoperative complication of Hirschsprung's disease (HD). Probiotics potentially play a protective role in maintaining intestinal mucosal integrity. Based on the beneficial effects of probiotics, we hypothesized that oral probiotics could decrease the incidence and severity of Hirschsprung's disease-associated enterocolitis (HAEC). Methods We conducted a prospective, multicenter, randomized, and controlled trial to assess whether oral probiotics could decrease the incidence and severity of HAEC. HD patients were randomly assigned into the control group and probiotic-treated group. All children in probiotic-treated group were fed with probiotics per day for 4 weeks. In next 3 months, the incidence and severity of HAEC were analyzed. The peripheral blood T lymphocyte subsets and cytokines, including TNF-alpha, IFN-gamma, IL-6, and IL-10, were analyzed by flow cytometry and enzyme immunoassay (EIA). Results Compared with the control group, the incidence of HAEC in the probiotic-treated group was significantly diminished. The severity of EC was also remarkably decreased. Furthermore, probiotics balanced T lymphocyte subsets. Moreover, pro-inflammatory cytokines TNF-alpha, IFN-gamma, and IL-6 were significantly decreased and anti-inflammatory cytokine IL-10 was notably increased in probiotic-treated group. Conclusions Probiotics not only significantly diminished the incidence but also decreased the severity of HAEC. Moreover, our study revealed that probiotics decreased pro-inflammatory cytokine and increased anti-inflammatory cytokine and furthermore balanced T lymphocytes (registered with ClinicalTrials.gov, NCT number: NCT01934959).