Abstract: OBJECTIVE To study the clinical effects to neonatal infectious pneumonia using different antibiotics and the impact to intestinal microflora,in order to provide a theoretical basis for clinical treatment.METHODS A total of 180 newborns with infectious pneumonia from our hospital between Sep.2014 to Sep.2015 were chosen,who were divided into three groups,according to the application of different drugs,60 cases with cephalosporin group,58 cases penicillin group and 62 patients combined treatment group,and the clinical cure rate and cure time for each group of children were compared.While 80 healthy patients were chosen as a control group,and the gut microflora environment in each group were observed.RESULTS The cure rate in patients in cephalosporin group was73.3%,penicillin group 72.4%,the combined treatment group 74.2%,no significant difference in the cure rate of the three groups.Cephalosporin group of patients with clinical cure time was（5.4±0.3）d,penicillin group（5.6±0.3）d,combination therapy group（5.3±0.4）d,the three groups showed no difference in healing time.Treatment group were significantly lower than the number of Bifidobacteriain the control group,and the difference was significant（P＜0.05）.The number of Enterobacteriaceae,Peptostreptococcus and Enterococci in patients with drugs were significantly higher than the control group（P＜0.05）.Bacteroides number had no significant difference.CONCLUSION The treatment in combination was preferred in neonatal pneumonia antibiotics treatment,but the combination treatment will cause damage to intestinal microflora newborns and break the normal state of equilibrium,therefore antimicrobial drugs should be rational used in clinic.