In order to investigate the efficacy of mosapril citrate combined with ShenQu Xiaoshi oral liquid in the treatment of children with functional dyspepsia and the effect on serum cytokines, 136 children with functional dyspepsia admitted from May 2017 to September 2020 were divided into 2 groups randomly, 68 cases in each group. The western medicine group was treated with mosapril citrate tablets, and the combined group was treated with Shenqu xiaoshi oral liquid on the basis of the western medicine group. The efficacy of patients was evaluated 14 days after treatment, and the safety, symptom score, and serum cytokines of the two groups were compared. The results showed that, after 14 days of treatment, the scores of abdominal distension and abdominal pain (ADAP), lack of food (LOF), nausea and vomiting (NAV), irregular stool (IS), and mental fatigue (MF) in the combined group were all lower than those in the western group (). There was no statistical significance in the incidence of diarrhea, abnormal liver and kidney, and allergic rash between the two groups (). In conclusion, mosapride citrate tablets combined with Shenqu Xiaoshi oral liquid can achieve good therapeutic effects in children with functional dyspepsia, reduce symptom scores, improve serum cytokine levels, and have high drug safety, which is worthy of promotion and application.