Background: Although one lung ventilation (OLV) is commonly used, little is known about the modulation of the autonomic nervous system with OLV while under general anesthesia. As the frequency domain and time domain analyses are powerful analytic tools, we investigated their modulation during OLV. Methods: Patients undergoing thoracic surgery were classified into two groups: those who did (group A, n=8) and those who did not (group N, n=8) receive atropine. After a double lumen tube was placed endotracheally, mechanical ventilation of both lungs (BLV) was established at 18 min−1 while under isoflurane anesthesia. Electrocardiogram, systolic arterial pressure (SAP), and inspiratory flow (Finsp) were digitally recorded as follows: awake before anesthesia; BLV after anesthesia; BLV after intravenous 10 µg kg−1 of atropine (group A) or not (group N); left OLV; and right OLV. Power spectral analyses of heart rate (HR) and SAP were computed by determining low-(LF, 0.04–0.15 Hz) and high-frequency (HF, 0.15–0.40 Hz) components, and impulse response analysis was executed among HR, SAP, and Finsp. Impulse responses were assessed by the maximum values in the time domain. Results: In frequency domain analysis, atropine depressed LF and LF/HF but not HF in HR variability, while no difference was observed between right OLV and left OLV. The heart rate to SAP impulse response was maintained at a significantly higher level in group A than in group N (905±360 vs. 425±375 mmHg beats−1min−1) at right OLV. A significant difference was also observed between left and right OLV within group N. Conclusion: Impulse response analysis demonstrated that there is a greater effect on autonomic nervous system modulation during right OLV than in left OLV, which mainly results from a parasympathetic neural linkage origin.