Gold nanostructures play a crucial role in medical applications, harnessing size and shape‐dependent properties. A prominent area of research is cancer treatment through the photothermal approach. Here, numerical simulation is explored to study the impact of gold nanostructure size, shape, and laser parameters on spatiotemporal temperature patterns during photothermal therapy (PTT). Spherical, rod, star, bipyramid, and cubic nanostructures in small, medium, and large sizes underwent 150 s of laser irradiation. COMSOL software, incorporating bioheat physics, precisely gauged thermal variations. The structural characteristics notably influence the temperature profiles, with medium‐sized rod, star, and bipyramid gold nanoparticles exhibiting superior thermal properties. Experimental validation of simulations focuses on the optimal nanostructure, synthesizing through the seed growth method. Transmission electron microscopy, UV‐visible spectroscopy, and X‐ray diffraction analysis confirm its proposed characteristics. Results demonstrate a robust correlation between experimental and simulation parameters, affirming precision. Findings showcase photothermal properties in line with theoretical predictions. The aim of this study is to determine the optimal gold nanostructure for bone cancer treatment using PTT, addressing the challenges presented by the dense and resilient nature of bone tissue and deep tumor locations. By utilizing multi‐physical modeling and simulations facilitated by COMSOL software, a novel method for pre‐clinical estimation is introduced. This research provides insights into each nanoparticle‐based PTT process prior to ex vivo and in vivo studies, offering a comprehensive understanding of the interplay between nanostructure characteristics and PTT outcomes. The approach contributes to advancing the field of cancer treatment by enhancing the predictability and effectiveness of nanoparticle‐mediated PTT.