To observe the efficacy of auto-trilevel positive airway pressure (Auto-trilevel PAP) ventilation in overlap syndrome (OS) patients with hypercapnia. From October 2012 to May 2014, 21 OS patients with a PaCO2> 45 mmHg (1 mmHg = 0.133 kPa) and coexisting stable chronic obstructive pulmonary diseases (COPD) and moderate-to-severe OSAS were recruited. Three different positive airway pressure (PAP) modes of ventilators (SOMNOvent auto-S, Weinmann Inc, Germany) were employed for 8 hours per night with each mode at each night and two nights' interval without any treatment among different modes. Under mode one, the expiratory positive airway pressure (EPAP) issued by bilevel positive airway pressure (BiPAP) was titrated as the minimal positive pressure for a disappearance of snoring. The same inspiratory positive airway pressure (IPAP) titrated by end tidal CO2 levels under mode 1 was used under modes 2 and 3 as well. However, the EPAP issued by BiPAP under mode 2 was 3 cmH2O (1 cmH2O = 0.098 kPa) higher than that under mode 1. Under mode 3 with autotrilevel PAP, the beginning of EPAP was set the same as that under mode 1 while the end of EPAP (EEPAP) was automatically adjusted based on upper airway patency condition. Comparisons were made for parameters before and after treatment as well as among different ventilation modes. The following parameters were compared such as nocturnal apnea hypopnea index (AHI), minimal SpO2 (miniSpO2), arousal index, sleep efficiency, morning PaCO2 and Epworth sleepiness score (ESS). Compared with the parameters pre-therapy, modes 1-3 showed a significant decrease in nocturnal AHI (6.3 ± 1.3), (3.1 ± 1.0), (3.6 ± 0.6) vs (38.6 ± 11.3) events/h), arousal index ((7.0 ± 1.1), (5.1 ± 0.9), (4.2 ± 1.7) vs (27.5 ± 5.4) events/h), morning PaCO2 (42.4 ± 3.8), (47.9 ± 2.6) and (43.2 ± 3.3) vs (57.3 ± 4.3) mmHg and daytime ESS (7.2 ± 1.3, 7.4 ± 1.3 and 5.3 ± 1.5 vs 11.4 ± 2.7), but a significant increase in nocturnal miniSpO2 (82.3 ± 5.4), (89.6 ± 3.9) and (90.3 ± 3.2) vs (62.4 ± 11.3) mmHg and sleep efficiency caused (71.3 ± 5.2)%, (79.4 ± 4.3)% and (83.2 ± 4.4)% vs (59.8 ± 6.3)% (all P < 0.01). Comparison of 3 modes demonstrated that, with the same IPAP, mode 3 resulted in the lowest arousal index, daytime ESS and the highest sleep efficiency. Comparison of modes 1 and 2 revealed a statistically lower AHI but higher miniSpO2 and morning PaCO2 under mode 2 (all P < 0.01). Compared with mode 1, mode 3 showed a lower AHI, higher miniSpO2 (all P < 0.01), but there was no significant difference in PaCO2 at the end of therapy. Compared with mode 2, mode 3 showed a significant lower PaCO2 (P < 0.01), but there was no significant difference in AHI and miniSpO2. Auto-trilevel PAP ventilation is superior to fixed BiPAP ventilation in the treatment of hypercapnic OS since this novel PAP mode can achieve a higher efficacy in simultaneous removal of residual apnea hypopnea events and correction of hypercapnia and yield a higher sleep quality and lower daytime sleepiness.