BACKGROUND: Isolated REM sleep behavior disorder (iRBD) is a prodromal stage of α-synucleinopathies, including Parkinson's disease (PD). Conventional sleep staging assigns each epoch to a single dominant stage, potentially obscuring within-epoch probabilistic features and stage mixing. We aimed to characterize alternation of probabilistic sleep-stage patterns in iRBD and to examine their clinical and neurobiological correlations. METHODS: In this case-control study, 104 patients with iRBD, 28 patients with PD and RBD (PD + RBD), and 50 controls underwent video polysomnography. Sleep-stage uncertainty and mixing were quantified using the U-Sleep 2.0 model. Clinical measures included RBD symptom severity (RBDQ-HK), motor function (UPDRS-III), and cognition (MoCA). Nigrostriatal dopaminergic function was assessed with [18F]-DOPA PET in a subgroup consisting of 40 patients with iRBD. Within the iRBD group, associations between probabilistic sleep-stage metrics and mixing with clinical measures and PET metrics were assessed using Pearson correlations. RESULTS: Both iRBD and PD + RBD groups exhibited significantly increased sleep-stage uncertainty and mixing compared with controls. Within the iRBD group, REM uncertainty was positively correlated with RBD symptom severity (RBDQ-HK score, r = 0.364, p = 0.003) and motor symptoms (UPDRS-III score, r = 0.343, p = 0.005). N2 uncertainty was negatively correlated with global cognitive performance (MoCA score, r = -0.345, p = 0.005), particularly delayed recall (r = -0.402, p < 0.001). N2-REM mixing was positively correlated with RBD symptom severity (RBDQ-HK score, r = 0.449, p < 0.001) and negatively correlated with bilateral putaminal dopaminergic uptake on PET (left: r = -0.492, p = 0.019; right: r = -0.510, p = 0.019). CONCLUSIONS: Probabilistic sleep staging reveals clinically significant alterations in sleep-stage uncertainty and stage mixing in iRBD and may provide complementary electrophysiological markers of early α-synuclein-related neurodegeneration.