Thuja (Thuja sutchuenensis Franch.) (family Cupressaceae) is a Chinese endemic plant once declared extinct in China. After being rediscovered in 1999, it attracted the attention of domestic scholars. This study aimed to investigate the extraction process and composition of the essential oil from thuja to provide a reference for further research. The main xylem of thuja collected from the Qinling‐Bashan mountains was used as the experimental material. The essential oil of thuja was extracted by the supercritical carbon dioxide fluid extraction (SFE‐CO2) process, and the composition of the essential oil was detected by gas chromatography‐mass spectrometry (GC‐MS). Extraction pressure, extraction temperature, and extraction dynamic time were the main factors influencing the extraction rate. The optimal conditions for the extraction include the following: maintaining the extraction pressure at 20 MPa, extracting for 60 min at 45 °C, and maintaining the CO2 flow rate at 1.5 L min–1 at 120 °C. Under the optimal extraction conditions, the oil extraction rates of three verification experiments were 18.87, 18.63, and 19.07%. The GC‐MS detected 136 components from the extracted thuja essential oil, and 75 components were identified. The main components of the essential oil were cis‐thujopsene (23.54%) and cedrol (13.08%). In this study, the optimal process for SFE‐CO2 of essential oil from the xylem of thuja was obtained. Under this optimized process, the average oil content was 18.86%.