The research examines how silica aerogel and paraffin behaved as phase-change materials in thermal energy storage systems using CuO nanoparticles. The significance is in meeting the need for effective energy storage techniques in response to increasing air pollution levels and rising conventional fuel expenses. The study used molecular dynamics simulations to examine the atomic and thermal properties of a silica aerogel/paraffin/CuO nanostructure within a cylindrical duct. This modeling setup allows for a comprehensive exploration of the interactions among different materials within the thermal energy storage system, offering insights into their combined effects on thermal performance and efficiency. Key results include a nanostructure reaching a maximum (Max) velocity (Velo), temperature (Temp), and density of 0.0096 Å/fs, 626 K, and 0.1365 atom/Å3. The thermal performance represented a sample exhibiting a thermal conductivity and heat flux of 1.74 W/m.K and 66.43 W/m2. The significance of this study utilizing the proposed model lied in its potential to advance our understanding of thermal energy storage systems and their applications. Through an examination of the atomic and thermal behavior of silica aerogel/PCM when CuO nanoparticles were present in a cylinder duct, this study made a valuable contribution to the advancement of energy storage solutions that were both more efficient and effective. The findings of this study may serve as a potential for innovative developments in thermal energy storage and aid in the creation of more environmentally friendly and functional energy solutions.