Electron–phonon coupling thermal resistance in metals is a key factor affecting the thermal boundary conductance (TBC) of metal–metal–dielectric systems. However, quantitatively differentiating the contribution of electron–phonon coupling to TBC is still a challenge, as various thermal resistances are coupled in a complicated manner at the metal–metal–dielectric interface. Herein, we propose a two-step strategy to study electron–phonon coupling. We first decouple the phonon–phonon thermal conductance (TBCp-p) between metallic interlayer and dielectric from the metal–metal–dielectric interface by experimentally characterizing the TBCp-p of a single metallic interlayer deposited dielectric with the transient thermoreflectance technique; Combining metal–metal–dielectric TBC measurement and a thermal circuit model with measured TBCp-p as input, the contribution of electron–phonon coupling to TBC of the metal–metal–dielectric system is differentiated quantitatively. For the Au–Ni–GaN system, the contribution of electron–phonon coupling thermal resistance in the Ni interlayer (Re−ph,Ni) is substantially higher at lower Ni interlayer thickness, reaching 35% at ∼1 nm Ni. The electron–phonon coupling constant of Ni (gNi) was fitted in the range of 6.4 × 1016–36 × 1016 W/m3K. The above results were also verified in the Au–Ni–SiC system. This study will promote a deeper understanding of the thermal transport in the metal–metal–dielectric system and provide an insightful indication for the manipulation of TBC in this system.