Ventilator associated pneumonia (VAP) is an infectious disease with high incidence rate and mortality in intensive care unit (ICU). The traditional etiological diagnosis method usually takes more than 24 h, delaying the treatment time and resulting in a mortality rate of up to 10%. In this study, we tried to achieve the rapid screening of VAP using exhaled volatile organic compounds (VOCs). The breath samples of 42 patients with VAP and 32 uninfected people from ICU were collected through intubation sampling and detected using a proton transfer reaction-mass spectrometry (PTR-MS). The collection and detection process only took less than 10 min. And then, Mann Whitney U test and stepwise discriminant analysis were used to discover the characteristic ions of VAP, which can be used to discriminate the two groups. Finally, we cultured five major pathogens (P. aeruginosa, K. pneumoniae, A. baumannii, E. coli and S. maltophilia) from VAP patients. The relationships between exhaled VOCs from the infected patients and VOCs released by the five pathogens were analyzed. The results showed that exhaled acetaldehyde could be used alone for screening VAP. The sensitivity and specificity were 71.4% and 84.4%, respectively, and the area under the curve (AUC) obtained by receiver operating characteristics (ROC) analysis was 0.796. We also found a large amount of acetaldehyde was produced by the five pathogens in the process of proliferation. Moreover, the content of exhaled acetaldehyde was positively correlated with the number of pathogens. So, we speculated the VAP biomarker acetaldehyde in the exhaled breath was mainly originated from these pathogens. In conclusion, the rapid screening of VAP can be achieved through detection of exhaled acetaldehyde using PTR-MS, which can assist doctors making treatment strategies in time.