The urgent challenges posed by the energy crisis, alongside the heat dissipation of advanced electronics, have embarked on a rising demand for the development of highly thermally conductive polymer composites. Electrospun composite mats, known for their flexibility, permeability, high concentration and orientational degree of conductive fillers, stand out as one of the prime candidates for addressing this need. This study explores the efficacy of boron nitride (BN) and its potential alternative, silicon nitride (SiN) nanoparticles, in enhancing the thermal performance of the electrospun composite thermoplastic polyurethane (TPU) fibers and mats. The 3D reconstructed models obtained from FIB-SEM imaging provided valuable insights into the morphology of the composite fibers, aiding the interpretation of the measured thermal performance through scanning thermal microscopy for the individual composite fibers and infrared thermography for the composite mats. Notably, we found that TPU−SiN fibers exhibit superior heat conduction compared to TPU−BN fibers, with up to a 6 °C higher surface temperature observed in mats coated on copper pipes. Our results underscore the crucial role of arrangement of nanoparticles and fiber morphology in improving heat conduction in the electrospun composites. Moreover, SiN nanoparticles are introduced as a more suitable filler for heat conduction enhancement of electrospun TPU fibers and mats, suggesting immense potential for smart textiles and thermal management applications.