Objective: To establish a multiplex PCR combined with capillary electrophoresis system for the detection of mycoplasma pneumoniae (MP), Staphylococcus aureus (S. Au), Klebsiella pneumoniae (KP), Pseudomonas aeruginosa (P.Ae), Cloacae bacilli (ECL), Candida albicans (CAL) and Acinetobacter baumannii (ABA), seven pathogens of children's lower respiratory tract. Methods: Pathogen samples of lower respiratory tract from 266 children were randomly collected from November 2020 to December 2020 in Nanjing Children's Hospital. Specific primers were designed for conservative sequences of MP, s.a u, KP, P.A, ecl, CAL and aba. The detection system of multiplex PCR combined with capillary electrophoresis was designed and optimized, the detection results were compared with bacterial culture and fluorescence quantitative PCR to evaluate the detection performance (sensitivity and specificity) of the method. Results: The designed primers can specifically amplify the pathogens of lower respiratory tract.The detection limit of multiplex PCR combined capillary electrophoresis detection system was 10 3 copies/L, CV were all < 10%.Other pathogens of lower respiratory tract infection showed no cross reaction, no obvious non-specific heteropeaks and good specificity. Conclusion: A multiplex PCR combined with capillary electrophoresis method was successfully developed to rapidly screen 7 common pathogens in children's lower respiratory tract.