Objective: To explore the clinical efficacy of anti-infective therapy based on upper respiratory tract targeted pathogen sequencing in children with severe community-acquired pneumonia (CAP). Methods: A total of 160 children with severe CAP were selected as the research subjects. According to the treatment methods, all children were divided into control group (n=80) and observation group (n=80). The control group received conventional anti-infective treatment, and the observation group received anti-infective therapy based on upper respiratory tract targeted pathogen sequencing. The pathogen detection results, efficacy, treatment time, medical cost, and incidence of adverse reactions were compared between two groups. Results: The positive rate of the observation group was higher than that of the control group (88.75% vs. 76.25%, P<0.05). Compared with control group, the positive rate of viruses, mycoplasma, and two or more pathogens in the observation group were increased (P <0.05). In the main detected pathogens, the number of adenovirus and mycoplasma pneumoniae in observation group were higher than those of control group (P<0.05). The effective rate in the observation group was higher than that in the control group (P<0.05). The number of cases with treatment regimen adjustment in the observation group was higher than that in the control group (P<0.05). Compared with control group, the duration of antibiotic usage, length of hospital stay, and medical costs in the observation group were reduced (P <0.05). There was no statistically significant difference in adverse reactions between the two groups (P>0.05). Conclusion: Upper respiratory tract targeted pathogen sequencing could quickly and accurately identify the pathogen of children with severe CAP, the anti-infective treatment based on its guidance can effectively improve clinical efficacy, shorten hospitalization time and antibiotic use time, and reduce medical costs.