Background Delirium is a primary adverse event in ventilated patients who receive long-term monosedative treatment. Sequential sedation may reduce these adverse effects. This study evaluated risk factors for delirium in sequential sedation patients. Methods A total of 141 patients who underwent sequential sedation were enrolled. Delirium was diagnosed using Confusion Assessment Method for the Intensive Care Unit (CAM-ICU) scale. Univariate and multivariate Cox proportional hazards regressions were used to predict risk factors. Results Older age (≥51) (RR = 2.432, 95% CL 1.316–4.494, p = 0.005), higher SOFA score (≥14) (RR = 2.022, 95% CL 1.076–3.798, p = 0.029), regular smoking (RR = 2.366, 95% CL 1.277–4.382, p = 0.006), and higher maintenance dose of midazolam (RR = 1.052, 95% CL 1.000–1.107, p = 0.049) and fentanyl (RR = 1.045, 95% CL 1.019–1.072, p = 0.001) when patients met sequential criteria, were independent risk factors of delirium. Sequential sedation with dexmedetomidine (RR = 0.448, 95% CL 0.209–0.963, p = 0.040) was associated with a lower risk of delirium. Conclusions Older age, higher SOFA score, regular smoking, and higher maintenance dose of midazolam and fentanyl when patients met sequential criteria were independent risk factors of delirium in sequential sedation patients. Sequential sedation with dexmedetomidine reduced risk of delirium.