The role of phonons in cuprates remains controversial, with their complex lattice structure complicating the investigation. Here, we identify phonon modes originating from charge reservoir and superconducting layers of Bi2Sr2CaCu2O8+δ using sub-unit-cell resolved electron energy loss spectroscopy in a scanning transmission electron microscope. We reveal several phonon modes exhibiting layer-specific localization: ~78 meV in-plane modes localized in the CuO2 planes, ~42 meV hybrid (in-plane and out-of-plane) modes in the CuO2 planes, and ~38 meV hybrid modes in the BiO layers. We also observe a periodic modulation of phonon frequencies induced by the superstructure, spatially correlating with the superconducting gap variation. Our findings offer new insights into the electron-phonon coupling in cuprates, fostering deeper exploration of the microscopic linkage between lattice dynamics and superconductivity.

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