The Moiré superlattices in twisted two-dimensional materials give rise to extraordinary electronic and thermal properties. While twist-angle tuning has been extensively explored for electronic applications, its synergistic effects with substrate coupling on thermal transport remain less understood. This study decouples the distinct roles of in-plane and out-of-plane phonons in the thermal conductivity of twisted bilayer graphene supported by a substrate. We demonstrate that increasing the twist angle enhances the inhomogeneity of the local stacking structure at small angles, leading to a rapid decrease in the contribution of out-of-plane phonons. In contrast, the in-plane phonon contribution exhibits remarkable structural stability, showing only minor variation. Furthermore, substrate coupling induces a pronounced layer-dependent modulation: The out-of-plane phonon contribution in the substrate-adjacent layer (Layer 2) is significantly suppressed due to constrained vibrations, while its in-plane contribution is enhanced by a more uniform stress distribution. Through atomic-scale analysis of interaction energies and stress, we spatially identify the primary scattering centers: AA stacking and saddle point (SP) stacking domains for out-of-plane phonons, and SP domains for in-plane phonons. These findings elucidate the synergistic mechanism by which twist angle and substrate coupling regulate thermal transport, providing crucial theoretical guidance for the design of thermal management systems and functional devices based on twisted two-dimensional materials.

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• Heat transfer
• Phonons
• Thermal conductivity
• Twisted bilayer graphene
• Molecular dynamics