The volatile components between stems and roots and also among five Clematis species from China were studied and analyzed by gas chromatography-mass spectrometry (GC-MS) combined with alternative moving window factor analysis (AMWFA), a new chemometric resolution method. Identification of the compounds was also assisted by comparison of temperature-programmed retention indices (PTRIs) on HP-5MS with authentic samples included in our own laboratory database under construction. A total of 153 different compounds accounting for 86.6-96.5% were identified and significant qualitative and quantitative differences were observed among the samples. The major volatile components in different essential oils from Clematis species were n-hexadecanoic acid and (Z,Z)-9,12-octadecadienoic acid. Our work further demonstrated chemometric resolution techniques upon the two-dimensional data and PTRIs can provide a complementary and convenient method for fast and accurate analysis of complex essential oils.