Patients with Eisenmenger syndrome (ES) have a higher mortality rate than patients with simple congenital heart disease (CHD). To determine factors associated with death in the era of advanced pulmonary vasodilator treatment, we analyzed the characteristics of adult ES patients depending on underlying CHD. Simple septal defects and patent ductus arteriosus were classified as simple CHD, and other conditions were classified as complex CHD. Sixty-seven adult ES patients (50.7% women) were reviewed retrospectively. CHD was diagnosed at a median of 10.0 years of age and ES was diagnosed at 18.6 years. Thirteen patients (19.4%) died; the median age was 38.6 years (IQR 32.2–47.8). In a multivariate analysis, patients with SpO₂ < 85% had a higher mortality rate than others [hazard ratio (HR) 9.7; 95% confidence interval (CI) 1.002–95.2, p = 0.05]. In simple CHD patients, those with a low platelet count (< 100 × 10⁹/L) or low SpO₂ (< 85%) were at a higher risk of death than those without (HR 16.32, 95% CI 1.25–2266.31, p = 0.032; and HR 38.91, 95% CI 3.44–5219.41, p = 0.001, respectively). Advanced pulmonary vasodilators were used more in survivors than in non-survivors (48.1% vs. 15.4%, p = 0.032). Low SpO₂ and platelet count were related to mortality in adult ES, especially in those with simple CHD. Therefore, careful attention should be paid to the care of adult ES patients with this tendency; active pulmonary vasodilator treatment should be considered.