Comparative analysis of essential components in the herbal pair Radix Saposhnikoviae–Rhizoma seu Radix Notopterygii and its single herbs is performed using two-dimensional gas chromatography-mass spectrometry data coupled with a chemometric method, named alternative moving window factor analysis. Identification of the compounds is also assisted by comparison of temperature-programmed retention indices (PTRIs) on the OV-1 column with authentic samples. The experimental results show that the main volatile chemical components in the herbal pair are mainly from Rhizoma seu Radix Notopterygii, and the number of essential chemical components in the herbal pair is almost equal to the sum of the number in the two single herbs but with a different quantity.