Human sputum, a typical highly viscous biosample, was directly characterized at the molecular level using neutral desorption extractive electrospray ionization mass spectrometry (ND-EESI-MS) without multi-step sample pretreatment, in an attempt to provide a method for constructing the pattern recognition of rapid diagnosis of lung cancer. Under the optimal experiment conditions, glucose, amino acids, phosphoric lipids and other typical analytes in the sputum sample could be used to conduct qualitative or quantitative (in arginine) analysis. More interestingly, the full scan mass spectra from 50 patients of non-small cell lung cancer, recording the mass spectral fingerprints of sputum samples, were differentiated from the control group (50 healthy individuals) through principal component analysis (PCA). These findings suggest that valuable molecular information concealed in human sputum could be easily revealed and applied for conducting qualitative or quantitative analysis by direct ND-EESI-MS analysis.