Essential oils (EOs) are complex and susceptible to environmental conditions, they have a wide range of biological activities and are often used to differentiate between similar species. In this study, gas chromatography-mass spectrometry (GC–MS) coupled with chemometric analysis was applied to systematically analyse and evaluate EOs constituents and antioxidant activity of six Chinese Cupressaceae taxa (Platycladus orientalis Franco, P. orientalis Franco ‘Sieboldii’, P. orientalis Franco ‘Aurea’, Juniperus chinensis Roxb., J. chinensis Roxb. ‘Kaizuca’, and J. sabina L.) under identical conditions. The antioxidant activity of the EOs was evaluated using 2,2 -diphenyl-1-picrylhydrazyl (DPPH), 2,2’-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), and ferric reducing power (FRAP), and the total phenolic content (TPC) of the EOs was determined by Folin–Ciocalteau reagent. In total, seventy individual constituents were identified with the main components being α-pinene, sabinene, d-limonene, bornyl acetate, δ-3-carene and β-myrcene. Principal component analysis (PCA) and hierarchal cluster analysis (HCA) successfully discriminated the six taxa into three chemotypes and the unique chemotype revealed that J. chinensis ‘Kaizuca’ may be a species rather than a cultivar of J. chinensis. The results of OPLS-DA analysis showed that the three compounds screened, namely, α-pinene, sabinene, and δ-3-carene, can completely distinguish Platycladus spp. from Juniperus spp. The DPPH assay results ranged from 576.14 (J. chinensis ‘Kaizuca’) to 1146.12 (J. sabina) μmol eq Trolox/mL EO, while the ABTS values ranged from 1579.62 (P. orientalis ‘Aurea’) to 5071.82 (J. sabina) μmol eq Trolox/mL. In the FRAP assay, the values ranged from 1086.50 (J. chinensis ‘Kaizuca’) to 1191.18 (J. sabina) μmol eq Trolox/ml and the TPC of the EOs studied ranged from 15.17 (J. chinensis ‘Kaizuca’) to 39.37 (J. sabina) mg GAE/mL EO. The results consistently showed that J. sabina possessed the strongest antioxidant activity and can be preferentially used as a rich source of potentially natural antioxidants.