Abstract: Acute respiratory tract infections are the most common pediatric diseases with high incidence and mortality. At the same time, symptoms tend to be hidden and atypical due to the immaturity of the child’s immune system. In addition, lower respiratory tract specimens in children are not readily available, the etiological research has lagged behind, resulting in the difficulties of clinical diagnosis and irrational use of antibiotics in clinical, and causing great difficulties for respiratory tract infection with children prevention and control. With the rapid progress of molecular biology methods in recent years, the clinics have achieved remarkable results of the main pathogens of respiratory tract infection in children. Respiratory tract infections were caused by many pathogens, including viruses, bacteria, mycoplasma, etc. Traditionally, respiratory syncytial virus (RSV) is the most common pathogen, human rhinoviruses (HRV), influenza virus A and B (INF), parainfluenzaviruses 1, 2 and 3 (PIV) and adenovirus are also the major virus pathogens. The recently described human metapneumovirus (HMPV), human coronavirus (HCoV), human bocavirus (HBoV), human polyomavirus KI (KIV) and Wu virus (WUV) have been detected in samples collected from acute respiratory infection with children. Streptococcus pneumoniae (Sp) is the most common bacterial infectious pathogen, followed by Haemophilus influenzae (HI), Staphylococcus aureus (SA) and Moraxella catarrhalis (MC). In addition, Bordetella pertussis, Streptococcus pyogenes and gram-negative enteric bacteria are also common. Finally, Mycobacterium tuberculosis and Mycoplasma pneumoniae also account for a certain percentage. Pathogen detection is very important for the diagnosis of respiratory infections in children. In addition to traditional culture methods of pathogens, the progress of molecular biology techniques, especially polymerase chain reaction (PCR) technology appears, greatly improving the detection rate and detection time of pathogens.