Objective:To investigate the effect of automated nested multiplex PCR system in the detection of children with severe community-acquired pneumonia(CAP), and identify the pathogenic infection of the children with severe CAP in Foshan.Methods:Children with severe CAP, who were admitted to the PICU at Foshan First People′s Hospital from January 2016 to December 2018, were enrolled in the analysis.Nasopharyngeal secretions were collected.And automated nested multiplex PCR was used to detect adenovirus, coronavirus (HKUl type, NL63 type, 229E type, 0C43 type), human metapneumovirus, influenza A virus (H1 subtype, H1-2009 subtype, H3 subtype), influenza B virus, parainfluenza virus (type 1, type 2, type 3, type 4), respiratory syncytial virus, Bacillus pertussis, Chlamydia pneumoniae and Mycoplasma pneumonia.Results:Among the 290 specimens detected by the automated nested multiplex PCR, 246(84.83%) were positive.There were 166 positive samples for a single pathogen, 60 positive samples for two pathogens, 17 positive samples for three pathogens, and three positive samples for four pathogens.Among the virus-positive cases, respiratory syncytial virus was the most common pathogen in children younger than 6 months(62.39%, 73/117). The most common pathogen was human rhinovirus/enterovirus(43.48%, 20/46) from seven months to one year old.Adenovirus(37.50%, 18/48) was the most common pathogen among children aged one to three years old.Rhinovirus/enterovirus(35.00%, 7/20) was the most common pathogen among children aged three to six years old.The most common pathogen in children over six years old was influenza virus(46.67%, 7/15). The adenovirus detection rate was highest in May, the syncytial virus detection rate was highest in August, and the influenza virus detection rate was highest in July.Mycoplasma pneumoniae and pertussis were distributed throughout the year.Conclusion:The automated nested multiplex PCR system can detect multiple pathogens efficiently, quickly and accurately; the common pathogens of severe CAP are diverse in different age groups; the epidemic season of common pathogens is unique in different regions due to different climates.