Objective To investigate the effects of noninvasive ventilation with neurally adjusted ventilatory assist (NIV-NAVA) on the patient-ventilator synchrony degree, oxidative stress levels, and gas exchange effectiveness in patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD) and pulmonary encephalopathy. Methods A total of 102 patients with AECOPD and pulmonary encephalopathy were selected as the study subjects and randomly divided into a mechanical ventilation (MV) group or an NIV-NAVA group, with 51 cases in each group. The noninvasive ventilation-pressure support ventilation (NIV-PSV) mode was applied in the MV group, and the NIV-NAVA mode was applied in the NIV-NAVA group, and both groups were intervened for 3 days. The patient-ventilator synchrony degree, oxidative stress levels, gas exchange effectiveness, and successful weaning rate were compared between the two groups. Results The cycling delay time of inspiratory and expiratory and inspiratory trigger delay time in the NIV-NAVA group were shorter than those in the MV group (all P<0.05). Before the intervention, there was no statistically significant difference in serum glutathione, superoxide dismutase (SOD), or malondialdehyde level between the two groups (all P>0.05). After 3 days of the intervention, the serum glutathione and SOD levels in the two groups increased, and the serum glutathione and SOD levels in the NIV-NAVA group were higher than those in the MV group (all P<0.05); the serum malondialdehyde levels in the two groups decreased (all P<0.05), but the difference between the two groups was not statistically significant (P>0.05). There was no statistically significant difference in the level of arterial partial pressure of oxygen (PaO2) or arterial partial pressure of carbon dioxide (PaCO2) between the two groups before the intervention (all P>0.05). After 3 days of the intervention, the levels of PaO2 in the two groups increased, and the PaO2 level in the NIV-NAVA group was higher than that in the MV group; the PaCO2 levels in the two groups decreased, and the PaCO2 level in the NIV-NAVA group was lower than that in the MV group (all P<0.05). The final successful weaning rate of the NIV-NAVA group (94.12%) was higher than that of the MV group (70.59%) (P<0.05). Conclusion The application of NIV-NAVA in patients with AECOPD and pulmonary encephalopathy contributes to increasing patient-ventilator synchrony degree, improving oxidative stress response, strengthening gas exchange effectiveness, and enhancing the final successful weaning rate.