The atomic-scale nucleation mechanism of vapor-grown carbon nanofibers (CNFs) is investigated using classical molecular dynamics simulations with a developed parameterization. Carbon precipitation and graphene plane formation are simulated, taking into account the carbon concentration (CC) in Ni carbide. The simulated results show that the carbon atoms formed sp(2) networks or sp chains in the Ni nanocrystals and then precipitated onto the Ni surface with distinct precipitation dynamics and time intervals that are dependent on the CC. The lowest-energy configurations of the precipitated carbon atoms exhibit an irregular corrugated network, a defective graphene plane, and separate defective graphene planes under high, medium, and low CC, respectively. These observations are in good agreement with the microstructural characteristics of different types of CNFs from experiments. Pair correlation function calculations show that the precipitated carbon structures exhibit different graphite orderings. The study reveals the atomistic CNF nucleation mechanism and emphasizes the critical role of metal carbide CC in the microstructure formation of CNFs during synthesis.