Meniki (Chamecyparis formosensis) and Hinoki (C. obtusa) are precious conifers with excellent wood properties and distinctive fragrances that make these species popular in Taiwan for construction, interiors and furniture. In the present study, the compositions of essential oils prepared from Meniki and Hinoki were analyzed by gas chromatography-mass spectrometry (GC/MS). Thirty-six compounds were identified from the wood essential oil of Meniki, including Δ-cadinene, γ-cadinene, Δ-cadinol, α-muurolene, calamenene, linalyl acetate and myrtenol; 29 compounds were identified from Hinoki, including α-terpineol, α-pinene, Δ-cadinene, borneol, terpinolene, and limonene. Next, we examined the effect of Meniki and Hinoki essential oils on human autonomic nervous system activity. Sixteen healthy adults received Meniki or Hinoki by inhalation for 5 min, and the physiological and psychological effects were examined. After inhaling Meniki essential oil, participant's systolic blood pressure and heart rate (HR) were decreased, and diastolic blood pressure increased. In addition, sympathetic nervous activity (SNS) was significantly decreased, and parasympathetic activity (PSNS) was significantly increased. On the other hand, after inhaling Hinoki essential oil, systolic blood pressure, heart rate and PSNS were decreased, whereas SNA was increased. Indeed, both Meniki and Hinoki essential oils increased heart rate variability (HRV) in tested adults. Furthermore, in the Profile of Mood States (POMS) test, both Meniki and Hinoki wood essential oils stimulated a pleasant mood status. Our results strongly suggest that Meniki and Hinoki essential oils could be suitable agents for the development of regulators of sympathetic nervous system dysfunctions.