In the study of GaN/AlGaN heterostructure thermal transport, the interference of strain on carriers cannot be ignored. Although existing research has mainly focused on the intrinsic electronic and phonon behavior of the materials, there is a lack of studies on the transport characteristics of the electron-phonon coupling in heterostructures under strain control. This research comprehensively applies first-principles calculations and the Boltzmann transport equation simulation method to deeply analyze the thermal transport mechanism of the GaN/AlGaN heterojunction considering in-plane strain, with particular attention to the regulatory role of electron-phonon coupling on thermal transport. The study found that electron-phonon coupling increases additional phonon scattering and reorganizes phonon frequencies. Strain significantly regulates the degree of electron-phonon coupling in the GaN/AlGaN heterojunction, which is an effective strategy for controlling the thermoelectric properties of semiconductor materials, where compressive strain enhances coupling while tensile strain weakens it. In addition, in-plane stress causes the redistribution of interface charges, leading to the delocalization migration of electrons from Ga and Al regions to the N atoms, reducing localization. Compressive strain drives the migration of electrons from AlGaN to GaN, forming a more stable two-dimensional electron gas, while tensile strain inhibits this migration. Furthermore, compressive strain promotes the increase of phonon frequencies and the reduction of the bandgap, while tensile strain has the opposite effect. Strain optimizes the delocalization of phonon modes, enhancing the role of low-frequency phonons in interface thermal transport. At the same time, in-plane stress, especially compressive stress, suppresses ballistic phonon transport, affecting the non-equilibrium state of phonons. This study not only enriches the understanding of electron-phonon coupling phenomena in GaN/AlGaN heterojunctions but also provides a theoretical basis and guidance for the strain design and device application of semiconductor materials.