Phospholipid fatty acids play the crucial role in biophysical properties and the function of cellular membranes. In the present study, an accurate and sensitive method was developed to quantify phospholipid fatty acids in biological samples by using chemical isotope labeling coupled with atmospheric pressure gas chromatography quadrupole-time-of-flight mass spectrometry (APGC/Q-TOF MS). APGC, a soft ionization source, was operated under proton-transfer condition by introducing methanol into the ionization source as a modifier, which provided high quantifiable molecular ion peaks to substantially enhance the sensitivity. Fatty acid standards were methylated with methanol-d(4) to yield FAMEs-d(3) that were used as one-to-one internal standards to ensure accurate quantification. Thirty fatty acids in phospholipids were accurately quantified in wide linear range with limit of quantification ranging from 84.6 to 113.2 pg/mL. The newly developed method was successfully applied to quantify phospholipid fatty acids in brain and liver tissues from both fat-1 and WT mice. This method might be expanded to quantify free fatty acids or other conjugated fatty acids in biological samples or other matrices.