The demand for thermally resilient polymer systems has intensified with the advancement of high-performance electronics and energy applications, where materials must sustain elevated temperatures while maintaining structural and functional integrity. Polyether ether ketone (PEEK) has emerged as a leading high-performance thermoplastic due to its inherent thermal stability and mechanical strength, yet its thermal transport and crystallization behavior require further optimization for extreme operating conditions. This study presents a comparative thermal engineering analysis of PEEK nanocomposites incorporating titanium dioxide (TiO?) and zinc oxide (ZnO) nanoparticles, focusing on their influence on melting temperature, crystallinity, and molecular interaction mechanisms. At the macroscopic level, nanoparticle inclusion enhances thermal stability by restricting polymer chain mobility and promoting nucleation effects, leading to elevated melting temperatures and improved crystalline structure. At the microscopic scale, interfacial interactions between nanoparticles and the PEEK matrix govern energy transfer pathways, affecting both thermal conductivity and phase transition behavior. The findings demonstrate that TiO? and ZnO exhibit distinct roles in modifying crystallization kinetics and molecular ordering, with implications for tailoring material performance. This comparative framework provides critical insights into nanoparticle selection and design strategies for optimizing PEEK nanocomposites in advanced thermal management applications.