Polyunsaturated fatty acids (PUFAs) play a pivotal role in the biological effects, and are the potential biomarkers for some diseases. However, the structural diversity and similarity, the low concentration, and the interference of high abundant endogenous components challenge the PUFAs profiling. Herein, a novel analytical approach, off-line and on-line solid phase extraction-nano-liquid chromatography-quadrupole-time-of-flight mass spectrometry (off-line and on-line SPE-nano-LC-Q-TOF-MS), was established to monitor the PUFAs. The combination of off-line and on-line SPE removed most of impurities, and the recoveries ranged from 80.1% to 93.0% and the matrix effects were from 85.1% to 92.8%. Using this method, 51 PUFAs could be separated well and quantified with the limits of quantification between 0.006 and 2.2 pg. Finally, this developed method was applied successfully to simultaneously qualify and quantify the potential biomarkers in the allergic patients. 21 PUFAs including LTB4, 5S-, 11S-, 15S-HETE and 15S-HEPE showed significant differences. Our study indicated that the established method has the potential to sensitively and accurately determine the PUFAs in biological samples.