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Background: This study aimed to determine whether the hemodynamics of patients with right ventricle outflow tract obstructive congenital heart disease (RVOTO-CHD) improve after corrective surgery by changing the ventilation mode. Methods: Patients with RVOTO-CHD who underwent corrective surgery were enrolled in this study. Echocardiography and advanced hemodynamic monitoring were performed using the pulse indicator continuous cardiac output (PiCCO) technology in the pressure-regulated volume control (PRVC) mode, followed with switching to the pressure support ventilation (PSV) mode and neurally adjusted ventilatory assist (NAVA) mode in random order. Results: Overall, 31 patients were enrolled in this study from April 2021 to October 2021. Notably, changing the ventilation mode from PRVC to a spontaneous mode (PSV or NAVA) led to better cardiac function outcomes, including right ventricular cardiac index (PRVC: 3.19 ± 1.07 L/min/m2 vs. PSV: 3.45 ± 1.32 L/min/m2 vs. NAVA: 3.82 ± 1.03 L/min/m2, p < 0.05) and right ventricle contractility (tricuspid annular peak systolic velocity) (PRVC: 6.58 ± 1.40 cm/s vs. PSV: 7.03 ± 1.33 cm/s vs. NAVA: 7.94 ± 1.50 cm/s, p < 0.05), as detected via echocardiography. Moreover, in the NAVA mode, PiCCO-derived cardiac index (PRVC: 2.92 ± 0.54 L/min/m2 vs. PSV: 3.04 ± 0.56 L/min/m2 vs. NAVA: 3.20 ± 0.62 L/min/m2, p < 0.05), stroke volume index (PRVC: 20.38 ± 3.97 mL/m2 vs. PSV: 21.23 ± 4.33 mL/m2 vs. NAVA: 22.00 ± 4.33 mL/m2, p < 0.05), and global end diastolic index (PRVC: 295.74 ± 78.39 mL/m2 vs. PSV: 307.26 ± 91.18 mL/m2 vs. NAVA: 323.74 ± 102.87 mL/m2, p < 0.05) improved, whereas extravascular lung water index significantly reduced (PRVC: 16.42 ± 7.90 mL/kg vs. PSV: 15.42 ± 5.50 mL/kg vs. NAVA: 14.4 ± 4.19 mL/kg, p < 0.05). Furthermore, peak inspiratory pressure, mean airway pressure, driving pressure, and compliance of the respiratory system improved in the NAVA mode. No deaths were reported in this study. Conclusions: We found that utilizing spontaneous ventilator modes, especially the NAVA mode, after corrective surgery in patients with RVOTO-CHD may improve their right heart hemodynamics and respiratory mechanics. However, further randomized controlled trials are required to verify the advantages of spontaneous ventilation modes in such patients. Clinical Trial Registration: NCT04825054.