The volatile chemical constituents of Artemisia capillaries (an important traditional Chinese medicine) were determined by gas chromatography-mass spectrometry (GC-MS) and sub-window factor analysis (SFA). Seventy-five components were separated and 43 of them were qualitatively and quantitatively determined, which represented about 89.03% of the total content. This profile was then used to identify and assess the consistency of the herb by using an orthogonal projection method. Four different sources of A. capillaries were analyzed and compared with each other. Among the components determined, there were 51 components coexisting in all samples although the relative peak areas of a few showed variations. It is the first time to apply orthogonal projection method to the comparison of different samples, and it reduces the burden of qualitative analysis as well as the subjectivity. The results showed a fair consistency in their GC-MS fingerprint. A. capillaris was distinguished from Artemisia sacrorum L., a possible substitute in traditional Chinese medicine by comparing the fingerprints with each other.