Analysis of common volatile constituents in herbal pair (HP) Chuanxiong Rhizome (CXR)-Notoperygium root (NR) and its single herb was performed by the method of alternative moving window factor analysis (AMWFA). In total, 65, 71, and 79 volatile chemical components in volatile oil of CXR, NR, and HP CXR-NR were separately determined qualitatively and quantitatively, accounting for 83.69%, 96.04% and 95.39% total contents of volatile oil of CXR, NR, and HP CXR-NR respectively. Analysis by the method of AMWFA indicates that there are 45 common volatile constituents in HP CXR-NR and single herb CXR, and 63 common volatile constituents in HP CXR-NR and single herb NR and 31 common volatile constituents among these three systems. The experimental results also show that the number of volatile chemical components in HP CXR-NR is almost equal to the sum of the number in the two single herbs, and volatile chemical components in HP CXR-NR are mainly from single herb NR.