To improve the performance of PtRu/nitrogen-doped graphene composite carbon nanofibers, the composite carbon nanofibers were thermally compensated by deep cryogenic treatment (DCT), which realized the morphology reconstruction of composite carbon nanofibers. The effects of different DCT times were compared: 12 h, 18 h, and 24 h. The morphology reconstruction mechanism was explored by combining the change of inner chain structure and material group. The results showed that the fibers treated for 12 h had better physical and chemical properties, where the diameter is evenly distributed between 500 and 800 nm. Combined with Fourier infrared analysis, the longer the cryogenic time, the more easily the water vapor and nitrogen enter polymerization reaction, causing changes of chain structure and degradation performance. With great performance of carbonization and group transformation, the PtRu/nitrogen-doped graphene composite carbon nanofibers can be used as an efficient direct alcohol fuel cell catalyst and promote its commercialization.