Objective Shen-Ling-Bai-Zhu-San (SLBZS) is used for treating gastrointestinal disorders. However, the role of SLBZS in treating pneumonia in children is still unclear. Methods In this study, children (≥2 and <9 years) with pneumonia were treated with 0.1 g cefixime (cefixime group) or 0.1 g cefixime + 9 g SLBZS (SLBZS + cefixime). The drugs were administered twice daily for 10 days. The therapeutic effects of the two groups were compared. The white blood cell (WBC), neutrophil, and lymphocyte counts; neutrophil-lymphocyte ratio (NLR); serum inflammatory factor levels; and gut microflora were assessed. Results The clinical efficacy of SLBZS + cefixime treatment of pneumonia in children was higher than that of cefixime alone (93.3% vs. 86.7%). Both cefixime and SLBZS + cefixime treatments decreased the area of pulmonary inflammatory lesions, reduced white blood cell and neutrophil counts, neutrophil-lymphocyte ratio, inflammation, and increased lymphocyte count in children with pneumonia compared with those before treatment. Moreover, SLBZS enhanced the anti-inflammation and immunity-enhancing effects of cefixime in children with pneumonia. SLBZS + cefixime treatment decreased Enterobacter , Enterococcus , Bacteroides , and Fusobacterium counts and increased Bifidobacterium and Lactobacillus counts. Compared with the cefixime treatment group, the count of the six bacterial strains in the SLBZS + cefixime treatment group was closer to the normal level. Conclusion SLBZS enhanced the antipneumonia effect of cefixime in children with pneumonia by ameliorating gut microflora, inflammation, and immune response.