Pseudomonas aeruginosa frequently colonizes the lungs of chronic obstructive pulmonary disease (COPD) patients. Mucoid conversion is a hallmark of chronic P. aeruginosa infection, which is mediated by mucA gene mutations. The aim of this study is to identify predictive factors for mortality and the influence of mucA gene mutation in COPD patients with P. aeruginosa pneumonia. This study assessed 75 COPD patients with P. aeruginosa pneumonia at two university hospitals. The clinical and laboratory data were collected, and the P. aeruginosa isolates analyzed for the presence of mucA gene mutations. MucA gene mutation of P. aeruginosa was an independent predictor of mortality (odds ratio OR 10.43, 95% confidence interval CI: 1.53–70.90, p = 0.017). In addition, the APACHE II score and C-reactive protein/Albumin (CA) ratio were independent predictive factors for mortality (OR 1.25, 95% CI: 1.07–1.46, p = 0.004; and OR 1.06, 95% CI: 1.02–1.10, p = 0.003, respectively). The optimal cutoff value of CA ratio for the greatest sensitivity and specificity was calculated as 31.27 (sensitivity, 85.7%; specificity, 80.3%). CA ratio and mucA gene mutation of P. aeruginosa could be used as predictors to identify poor prognosis in COPD patients with P. aeruginosa pneumonia. •The presence of mucoid P. aeruginosa is associated with poor prognosis.•Mucoid conversion of P. aeruginosa is mediated by MucA gene mutation.•MucA gene mutation of P. aeruginosa is an independent predictor of mortality.