The Chinese government has issued the policy of promulgating the clinical use of antibacterial drugs since 2011. Prophylactic antibiotic use is a challenging problem among young children with intussusception after successful air enema reduction. There were limited data regarding the clinical value of prophylactic antibiotics for intussusception with low-risk infections. A retrospective non-randomized comparative study was conducted among 188 young children with intussusception after successful air enema reduction between January 1, 2011 and December 30, 2013. Among these children, 51 received prophylactic antibiotics and 137 did not receive antibiotics. Our results showed that there were no significant differences in age, gender, weight, admission period, reduction interval, axillary temperature, leukocytes, neutrophils, lymphocytes, monocytes, mesenteric lymph nodes and complications between groups (P > 0.05). The national policy had significantly improved clinical use of antibiotic for young children with low-risk intussusception (OR < 0.001, P < 0.001). Inpatients days were longer for children used antibiotics than those who did not (median, 27.0 hours vs 21.0 hours, P = 0.003). Prophylactic antibiotics appeared to be of little value after the successful air enema reduction of intussusception in young children with low-risk infection. Policy intervention is effective for antibiotic use in China.