The developing flexible electronic equipment are greatly affected by the rapid accumulation of heat, which is urgent to be solved by thermally conductive polymer composite films. However, the interfacial thermal resistance (ITR) and the phonon scattering at the interfaces are the main bottlenecks limiting the rapid and efficient improvement of thermal conductivity coefficients (λ) of the polymer composite films. Moreover, few researches were focused on characterizing ITR and phonon scattering in thermally conductive polymer composite films. In this paper, graphene oxide (GO) was aminated (NH2-GO) and reduced (NH2-rGO), then NH2-rGO/polyimide (NH2-rGO/PI) thermally conductive composite films were fabricated. Raman spectroscopy was utilized to innovatively characterize phonon scattering and ITR at the interfaces in NH2-rGO/PI thermally conductive composite films, revealing the interfacial thermal conduction mechanism, proving that the amination optimized the interfaces between NH2-rGO and PI, reduced phonon scattering and ITR, and ultimately improved the interfacial thermal conduction. The in-plane λ (λ∥) and through-plane λ (λ⊥) of 15 wt% NH2-rGO/PI thermally conductive composite films at room temperature were, respectively, 7.13 W/mK and 0.74 W/mK, 8.2 times λ∥ (0.87 W/mK) and 3.5 times λ⊥ (0.21 W/mK) of pure PI film, also significantly higher than λ∥ (5.50 W/mK) and λ⊥ (0.62 W/mK) of 15 wt% rGO/PI thermally conductive composite films. Calculation based on the effective medium theory model proved that ITR was reduced via the amination of rGO. Infrared thermal imaging and finite element simulation showed that NH2-rGO/PI thermally conductive composite films obtained excellent heat dissipation and efficient thermal management capabilities on the light-emitting diodes bulbs, 5G high-power chips, and other electronic equipment, which are easy to generate heat severely.