The chromatographic fingerprint of Fructus xanthii, a kind of Traditional Chinese Medicines (TCMs), was studied by microwave assisted extraction (MAE) coupled with gas chromatography-mass spectrometry (GC-MS). The optimized conditions of MAE were examined. The method of MAE was evaluated in contrast to heat reflux extraction (HRE) method and by the validation tests of precision and repeatability. The relative standard deviations (RSDs) of retention time and peak area of each component were less than 0.2% and 6%, respectively. Twenty-five different batches of samples collected from different producing areas and the toasting process of F. xanthii were studied. The characteristic differences in the producing areas and the chemical variances in the toasting process were obtained and studied by principal components analysis (PCA) and similarity analysis. The trends of main varying components were attempted to be described in order to specify the related pharmacology and toxicology in crude and toasted samples. The results suggest that the chromatographic fingerprint developed by MAE coupled with GC-MS provides useful information to reveal the quality of F. xanthii and evaluate the quality changes in the producing process.