Perillae Folium (PF), the leaf of Perilla frutescens (L.) Britt, is extensively used as culinary vegetable in many countries. It can be divided into two major varietal forms based on leaf color variation, including purple PF (Perilla frutescens var. arguta) and green PF (P. frutescens var. frutescens). The aroma of purple and green PF is discrepant. To figure out the divergence of chemical composition in purple and green PF, gas chromatography–tandem mass spectrometry (GC-MS) was applied to analyze compounds in purple and green PF. A total of 54 compounds were identified and relatively quantified. Multivariate statistical methods, including principal component analysis (PCA), orthogonal partial least-squares discrimination analysis (OPLS-DA) and clustering analysis (CA), were used to screen the chemical markers for discrimination of purple and green PF. Seven compounds that accumulated discrepantly in green and purple PF were characterized as chemical markers for the discrimination of the purple and green PF. Among these 7 marker compounds, limonene, shisool and perillaldehyde that from the same branch of the terpenoid biosynthetic pathway were with relatively higher contents in purple PF, while perilla ketone, isoegomaketone, tocopheryl and squalene on other branch pathways were higher in green PF. The results of the present study are expected to provide theoretical support for the development and utilization of PF resources.