The freezing of Ni nanowires at different cooling rates was studied by classical molecular dynamics simulation via embedded atom potential method. The structure evolution of Ni nanowires in the freezing region was also presented. In order to distinguishing the local clusters in the cooling process of Ni nanowires formed at different cooling rates the bond, pair analysis is employed. The simulation results indicate that the freezing of the nanowires starts from the surface and the structure of the nanowires changes from amorphous to fcc crystal via helical multi-shelled structure along with the decrease of cooling rate. The helical multi-shelled structure possesses not only the short-range order and long-range disorder of amorphous structure but also a definite crystallization temperature.