The three parts of Radix Angelicae Sinensis (Danggui) were reported to have different therapeutic effects. In order to investigate their chemical compositions of different parts of Danggui, gas chromatography-mass spectrometry (GC-MS) combined with chemometrics data analysis was applied to provide a more detailed study. Subwindow factor analysis (SFA) and a modified augmented evolving window orthogonal projection (AEWOP) method were used to resolve the batch GC-MS data sets from the Danggui samples. Then, t-test, Wilcoxon rank sum test, and principal component analysis (PCA) were applied to carry out the comparison job. The results indicate which components are found to have significant differences among the three parts. These findings may be helpful for further research of the pharmacological activities of Danggui.