Perilla frutescens is an important annual herb of the mint family that is native to East Asia, particularly China, Korea, and Japan, is widely used as a fresh vegetable and in traditional Chinese medicines, popular garnishes, and food colorants. Hydrodistilled essential oils obtained from P. frutescens from 11 areas of China were analyzed by gas chromatography-mass spectrometry (GC–MS). One hundred and nineteen compounds accounting for 98.07–99.74% of the oils were identified. The predominant compounds were 2-acetylfuran (max. 82.17%), perillaldehyde (max. 53.41%), caryophyllene (max. 38.34%), laurolene (max. 40.6%), 2-hexanoylfuran (max. 33.03%), 2-butylamine (max. 22.22%), α-asarone (max. 11.85%), β-farnesene (max. 9.25%), α-caryophyllene (max. 9.16%), and (Z,E)-α-farnesene (max. 7.14%). Chemical variation in the oils was estimated using cluster analysis and principal component analysis. The results revealed chemical polymorphism in the oils. However, the oils from Ganzhou, Kaili, Suining, Macheng, Nanyang, and Yixing were more similar, and the oils from Quzhou, Loudi, and Nanning also revealed similarities. Antioxidant activity (by free radical scavenging activity and ferric reducing power) and antifungal activity (by poisoned food method and micro-well dilution method) were also assessed. The antioxidant activity of the oils showed similar order to that obtained by three different testing methods: Pingliang, Baoding, Loudi, and Quzhou > Kaili, Ganzhou, Macheng, and Nanning > Suining, Nanyang, and Yixing. All oils except that from Baoding were active against all of the tested strains. These results suggested that the region of origin greatly influenced the chemical composition and bioactivities of P. frutescens, which might help in developing this promising bioresource in the food and pharmaceutical industries.