The essential oils of Juniperus are highly beneficial medicinally. The present study aimed to assess the chemodiversity and bioactivity of Juniperus formosana, Juniperus przewalskii, Juniperus convallium, Juniperus tibetica, Juniperus komarovii, and Juniperus sabina essential oils from the Qinghai-Tibet Plateau. The results revealed 92 components in six essential oils: α-pinene (2.71–17.31%), sabinene (4.91–19.83%), and sylvestrene (1.84–8.58%) were the main components. Twelve components were firstly reported in Juniperus oils, indicating that the geographical location and climatic conditions of the Qinghai-Tibet Plateau produced the unique characteristics of Juniperus essential oils. The chemodiversity of Juniperus essential oils varied greatly, with J. sabina having the most recognized components (64) and the highest chemodiversity (Shannon–Wiener index of 3.07, Simpson’s diversity index of 0.91, and Pielou evenness of 0.74). According to the chemodiversity of essential oils, the six plants were decided into the α-pinene chemotype (J. formosana), hedycaryol chemotype (J. przewalskii, J. komarovii, J. convallium, J. tibetica), and sabinene chemotype (J. sabina). PCA, HCA and OPLS-DA showed that J. formosana and J. sabina were distantly related to other plants, which provides a chemical basis for the classification of Juniperus plants. Furthermore, bioactivity tests exhibited certain antioxidant and antibacterial effects in six Juniperus oils. And the bioactivities of J. convallium, J. tibetica, and J. komarovvii were measured for the first time, broadening the range of applications of Juniperus. Correlation analysis of components and bioactivities showed that δ-amorphene, β-udesmol, α-muurolol, and 2-nonanone performed well in the determination of antioxidant activity, and α-pinene, camphene, β-myrcene, as well as (E)-thujone, had strong inhibitory effects on pathogenic bacteria, providing a theoretical basis for further research on these components.