This paper presents a numerical study of non-isothermal flow and heat transfer in an enclosed rotor–stator disk cavity. Wall-resolved large-eddy simulation is implemented with attention focused on the Reynolds number effect (Reϕ=105 and 5×105) and non-isothermal effects, including different thermal Rossby numbers (βΔT=0.05–0.25) and heat convection types (axial heat convection, axial and radial heat convection). Verification and validation are implemented by comparing with available experimental data and examining the resolution of the present LES. Although the Batchelor flow type is unchanged, the non-isothermal effect is found to be responsible for the acceleration of flow in both disk boundary layers and cavity core. Temperature in the cavity is negatively correlated with the Rayleigh number. The radial inward temperature gradient is found to be responsible for destabilizing the flow near the cylinders, due to the effect of centrifugal buoyant force. Transition from laminar to turbulent is shown in the rotor boundary layer for Reϕ=5×105 conditions. The non-isothermal effect increases flow unsteadiness in both rotor and stator boundary layers, but it has little to no effect on the transition position, as well as the kinematic and thermal boundary layer thicknesses, which are mainly controlled by Reϕ. Spectral proper orthogonal decomposition is implemented to explore the Reynolds number effect. Analyzing the most energetic mode and its energy spectra provides some insights into the understanding of non-isothermal rotor–stator disk cavity flows.