With the continuous increase in power density, operating frequency, and integration level of electronic devices, the heat flux generated in GaN-based devices rises rapidly, making thermal management a critical challenge that limits device reliability and performance. Interfacial thermal resistance (ITR) plays a key role in determining the overall heat dissipation effciency of heterostructures. In this work, the interfacial thermal transport properties of GaN/AlN heterostructures are systematically investigated using non-equilibrium molecular dynamics (NEMD) simulations. The effects of temperature, structural size, and vacancy defects on the ITR are analyzed in detail. The simulation results show that the ITR decreases monotonically as the temperature increases from 300 K to 700 K, which is mainly attributed to enhanced inelastic phonon scattering and the activation of additional phonon modes at elevated temperatures. The size-dependent analysis indicates that the ITR decreases significantly with increasing AlN layer thickness and gradually converges when the number of AlN layers reaches about eight. This behavior is closely related to the enhanced phonon coupling and improved phonon spectral matching across the interface. Furthermore, the introduction of vacancy defects on the GaN side near the interface leads to a non-monotonic variation in ITR. When the vacancy concentration increases from 0 to 5%, the ITR slightly decreases due to improved phonon transmission channels. However, further increasing the defect concentration up to 25% significantly enhances phonon scattering and lattice disorder, resulting in an approximately 11% increase in ITR. In addition, the influence of defect position is examined by varying the distance between the defect region and the interface. The results show that the ITR gradually decreases as the defect region moves away from the interface and becomes stable when the distance exceeds about 5 nm. By combining phonon density of states (PDOS) analysis with the phonon spectral overlap factor S, the underlying mechanisms governing interfacial phonon transport are clarified. The present work provides theoretical insights into the modulation of interfacial heat transport in GaN-based heterostructures and offers guidance for thermal management and interface engineering in high-power electronic devices.