Three Chamaecyparis species (C. formosensis, C. obtusa, and C. obtusa var. formosana) are difficult to distinguish by the naked eye. Therefore, from the chemotaxonomic point of view, it would be valuable to find a simple and rapid method to differentiate these three Chamaecyparis species. In this study, the chemical compositions of biogenic volatile organic compounds (BVOCs) from mature leaves were analyzed using solid-phase microextraction-gas chromatography/mass spectrometry (SPME-GC/MS). Then cluster analysis (CA) and principal component analysis (PCA) were conducted for the BVOC constituents to reveal the differences among these three species. Results from SPME-GC/MS showed that the compositions of BVOCs from the three species were distinctly different. Moreover, these species were clearly differentiated according to the results of CA and PCA. In conclusion, the findings of this study suggest that SPME-GC/MS coupled with CA and PCA is a feasible and rapid technique to differentiate Chamaecyparis species with similar morphological characteristics.