<p>The thermal diffusion behavior and temperature gradient response in three-dimensional (3D) gold nanoparticle (AuNP) arrays play a crucial role in photothermal regulation, biomedical applications, and the design of photothermal functional devices. In this work, a finite element method (FEM) is employed to systematically investigate how structural parameters influence thermal diffusion paths and temperature gradient distributions. The results reveal that under strong coupling conditions (small interparticle distance and large particle size), heat is highly concentrated in the center of the array, leading to intense local heating and asymmetric diffusion. As the spacing increases, the thermal diffusion pattern gradually evolves from “central accumulation–edge release” to a more uniform and extensive diffusion. Furthermore, the temperature gradient exhibits a decreasing trend across the layers, with the maximum temperature typically occurring in the upper-middle region, indicating an outward energy transfer from the center. In small-spacing configurations, the gradient transitions from positive to negative and reaches its maximum magnitude at the bottom layer, suggesting that heat is rapidly conducted from the center to the edges. This work establishes a coupled regulatory framework of “structural parameters–diffusion pattern–temperature gradient,” providing a theoretical foundation for the design and optimization of localized thermal regulation and directional heat diffusion in gold nanoparticle arrays.</p>