Comparative analysis of volatile constituents between recipe jingfangsan and its single herbs was performed by 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 the OV-1 column with authentic samples. In total, 36, 29, and 42 volatile components in essential oil of Herba schizonepetae (HS), Radix saposhnikoviae (RS), and the recipe were respectively determined qualitatively and quantitatively, accounting for 81.80, 82.62 and 85.98% total contents of volatile oil of HS, RS, and the recipe respectively. Analysis by the method of AMWFA indicates that there are 22 common volatile constituents between the recipe and single herbal medicine HS, and 14 common volatile constituents between the recipe and single herb medicine RS. The experimental results also show that the volatile components of the recipe in number are almost addition of that of two single herbal medicines HS and RS, and are mainly from the single herbal medicine HS.