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Due to the typical strong and tough graphitic structures, carbon nanofibers (CNFs) theoretically have excellent mechanical properties. However, in practice, the defects and misalignments in these crystal domains always jeopardize the performance of CNFs and limit their further application. In this case, this paper takes onion-like carbon (OLC) as an effective nanofiller to optimize the fiber graphitic structure and produces composite CNFs with enhanced strength and toughness. For this purpose, the in situ polymerization technique is specially developed for the rapid and uniform distribution of OLC in the polyacrylonitrile (PAN) precursor of CNFs. The obtained PAN-coated OLC nanoparticles successfully avoid the agglomeration of nanofillers and can be further electrospun into OLC uniformly doped PAN nanofibers. Owing to the interaction between OLC and PAN matrix, the crystal domains in PAN precursor nanofibers are thicker and transformed from integrated shish-kebab structures into nanofibril crystals with better regularity and orientation. In the subsequent stabilization and carbonization processes, these crystalline nanofibrils are considered to be the structural basis for the formation of oriented and continuous graphitic domains in final CNFs. Meanwhile, the graphitic shells of OLC are confirmed to act as the template in the carbonization process to induce and promote the crystallization of the surrounding fiber matrix and transform the turbostratic structures in fiber crystal domains into more orderly graphitic structures with increased size and continuity. Furthermore, the embedded nanoscale OLC can co-move and continuously interact with the resulting graphitic domains during the deformation process for load transfer. As a result, the tensile strength and elongation at break of OLC-reinforced CNFs increase by 53.5 and 34.0%, respectively. The strong and tough composite CNFs may help to avoid the potential fiber breaking in their practical use and be further applied in wearable capacitors, masks, filters, etc.