The similarities and differences of essential oil components in Pericarpium Citri Reticulatae Viride (PCRV) and Pericarpium Citri Reticulatae (PCR) were investigated by GC-MS combined with a chemometric method, named alternative moving window factor analysis (AMWFA). Furthermore, temperature-programmed retention indices (PTRIs) were used together with mass spectra for identification of the essential oil components. A total of 61 and 59 compounds in the essential oils of PCRV and PCR from three Citrus species were identified, which represented 98.15-99.66% and 97.6-99.84% of their total relative contents, respectively. The essential oils from PCRV and PCR significantly differed both qualitatively and quantitatively. The main compound in the essential oils from PCRV and PCR was d-limonene accounting for 65.61-83.14%. The comparative analysis indicates that AMWFA greatly enhanced the accuracy of quantitative and qualitative results by utilizing information from chromatography and mass spectra. The results obtained may be helpful to find out the possibly bioactive compounds of PCRV and PCR.