Objective To investigate the clinical efficacy of time-selected acupoint massage based on the midnight-noon ebb-flow theory combined with rectal infusion of the Qingfei Tiaochang Decoction in patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD) undergoing mechanically ventilation. Methods A total of 70 patients with AECOPD who received mechanical ventilation and were treated at the Hebi Hospital of Traditional Chinese Medicine from April 2023 to April 2025 were selected. They were randomly divided into a control group (n＝35, treated with rectal infusion of Qingfei Tiaochang Decoction) and an observation group (n＝35, treated with the control group""s method plus time-selected acupoint massage based on the midnight-noon ebb-flow theory). Clinical symptoms, arterial blood gas parameters, gastrointestinal hormone levels, and incidence of adverse reactions were compared between the two groups. Results After intervention, the observation group showed significantly lower scores on the modified Medical Research Council dyspnea scale (mMRC) and COPD assessment test (CAT) (both P＜0.05). The observational group exhibited significantly higher arterial partial pressure of oxygen (PaO2) and arterial oxygen saturation (SaO2), along with significantly lower arterial partial pressure of carbon dioxide (PaCO2), compared to the control group (all P＜0.05). The observation group exhibited significantly higher levels of substance P and motilin, but lower levels of vasoactive intestinal peptide (VIP) compared to the control group (all P＜0.05). No statistically significant difference was observed in the incidence of adverse reactions between the two groups (P＞0.05). Conclusion The combination of time-selected acupoint massage based on the midnight-noon ebb-flow theory and rectal infusion of the Qingfei Tiaochang Decoction can effectively reduce the severity of dyspnea in patients with AECOPD undergoing mechanical ventilation, alleviate disease symptoms, improve arterial blood gas parameters, modulate gastrointestinal hormone levels, and does not increase the risk of adverse events.