GaN/AlN superlattice structures have potential for high electron mobility transistors (HEMTs) applications; however, nonequilibrium phonon transport mechanisms within the superlattice have not been systematically investigated. Therefore, we investigate in detail the non-Fourier thermal conductivity of superlattice structures in the perpendicular interface direction and in the parallel interface direction around the phonon BTE numerical solution in this paper, taking the kinetic parameter based on the first principle as the input parameter of the equations and based on the DOM numerical solution scheme. The study reveals that mode temperature non-equilibrium in superlattices arises from ballistic transport within the layers and interface scattering between the layers. The thermal conductivity (TC) of superlattices can be modulated by scale effects, and in superlattices with small thicknesses, phonons exhibit quasi-ballistic transport. The interface thermal resistance predominantly originates from contributions by acoustic phonon (AP) and the first optical phonon (OP1). With increasing interface density, the combined effects of interface scattering and boundary scattering lead to strong phonon scattering, resulting in a decrease in TC parallel to the interfaces. This work provides valuable insights into the thermal transport properties of GaN/AlN superlattice semiconductors and offers useful theoretical guidance for thermal management through phonon particle properties.