Patient-ventilator asynchronies can be detected by close monitoring of ventilator screens by clinicians or through automated algorithms. However, detecting complex patient-ventilator interactions (CP-VI), consisting of changes in the respiratory rate and/or clusters of asynchronies, is a challenge. Sample Entropy (
SE
) of airway flow (
SE
-Flow) and airway pressure (
SE
-Paw) waveforms obtained from 27 critically ill patients was used to develop and validate an automated algorithm for detecting CP-VI. The algorithm’s performance was compared versus the gold standard (the ventilator’s waveform recordings for CP-VI were scored visually by three experts; Fleiss’ kappa = 0.90 (0.87–0.93)). A repeated holdout cross-validation procedure using the Matthews correlation coefficient (MCC) as a measure of effectiveness was used for optimization of different combinations of
SE
settings (embedding dimension,
m
, and tolerance value,
r
), derived
SE
features (mean and maximum values), and the thresholds of change (
Th
) from patient’s own baseline
SE
value. The most accurate results were obtained using the maximum values of
SE
-Flow (
m
= 2,
r
= 0.2,
Th
= 25%) and
SE
-Paw (
m
= 4,
r
= 0.2,
Th
= 30%) which report MCCs of 0.85 (0.78–0.86) and 0.78 (0.78–0.85), and accuracies of 0.93 (0.89–0.93) and 0.89 (0.89–0.93), respectively. This approach promises an improvement in the accurate detection of CP-VI, and future study of their clinical implications.