Background and Objectives The influence of virus detected in BALF is still debating. This study aimed to compare the prognosis of lower respiratory tract infected patients with virus detected in bronchial alveolar lavage fluid (BALF) and patients with virus undetected by using metagenomic next-generation sequencing technology.Methods This was a retrospective cohort study. 53 patients with lower respiratory tract infection were enrolled. BALF samples were collected from each patient and sent to perform mNGS pathogenic test in the study. According to the results of mNGS test, patients were divided into virus-detected group and virus-undetected group. In the meanwhile, patients’ clinical information, medical history, disease severity scores, parameters of organ function at the day of ICU admission, prognosis, hospital length of stay, ICU length of stay and needs for medical support were also collected.Results 39.6 percent (21/53) of the BALF samples were virus nucleic acid positive. Mortality rate, tracheotomy rate, mechanical ventilation supporting time, blood transfusion rate were significantly higher in virus-detected group than that in virus-undetected group. Virus-detected was closely related to hospital and ICU survival time.Conclusions Patients with virus detected in BALF were prone to a poorer prognosis. The detection of virus was a high-risk factor of death for LRTI patients. Virus-detected patients required more medical resources.