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Polymers are thermally insulating due to randomly oriented molecular chains, limiting their effectiveness in thermal management. However, when processed into nanofibers, polymers can exhibit significantly higher thermal conductivity, primarily due to enhanced internal structures such as crystallinity and molecular alignment. Characterizing these structural parameters at the single nanofiber level remains a challenge, limiting understanding of thermal transport mechanisms. Here, we investigate the relationship between internal structure and thermal conductivity of single polyethylene oxide (PEO) nanofibers fabricated from near-field electrospinning (NFES). By varying molecular weight and concentration of PEO, their impact on thermal conductivity and internal structure are examined. Crystallinity is examined using conventional Raman spectroscopy, while molecular orientation is assessed through polarized Raman and polarized FTIR spectroscopy. Results reveal that enhanced thermal conductivity in PEO nanofibers is primarily attributed to increased molecular orientation. A maximum thermal conductivity of 2.7 W/m·K is achieved in PEO nanofibers, representing a notable improvement over bulk PEO (0.2 W/m·K). These findings demonstrate the potential of structurally engineered PEO nanofibers for thermal applications including electronic packaging and thermal interface materials. Further, the approach presented in this work can provide a framework for exploring thermal transport mechanisms in other polymer systems.