To improve the mechanical properties of lignin based carbon nanofibers, the amine-terminated highly cross-linked polyphosphazene-functionalized carbon nanotubes (PZAA@CNTs) were successfully synthesized by in situ polycondensation and deposition using hexa-(4-aminophenoxy) cyclotriphosphazene (HACP) and hexachlorocyclotriphosphazene (HCCP) as monomers. The thickness of the amine-terminated polyphosphazene layer coated on the carbon nanotubes was about 12.7 nm. The strong interaction of hydrogen bonding between PZAA@CNTs and lignin facilitated the formation of good fiber morphology at various stages. The thin polyphosphazenes layer improved the thermal stability of lignin/PZAA@CNT-based nanofiber mats and promoted the carbonization of lignin. The tensile test results showed that significant enhancements of tensile strength and tensile modulus were achieved when 1.0 wt % PZAA@CNTs was introduced to lignin. X-ray diffraction (XRD) and Raman spectroscopy studies suggested that the number of graphite crystallites and crystallite size increased after incorporation of PZAA@CNTs. This is a promising method to enhance the mechanical properties of lignin-based carbon nanofibers and prepare biobased carbon nanofibers for a wider application.