A molecular dynamics simulation study has been performed for the microstructure evolution in a liquid metal Ni system during crystallization process at two cooling rates by adopting the embedded atom method (EAM) model potential. The bond-type index method of Honeycutt-Andersen (HA) and a new cluster-type index method (CTIM-2)have been used to detect and analyse the microstructures in this system. It is demonstrated that the cooling rate plays a critical role in the microstructure evolution: below the crystallization temperature Tc, the effects of cooling rate are different kinds of crystal structures are obtained in the system. The first one is the coexistence of the hcp (expressed by (12 0 0 0 6 6) in CTIM-2) and the fcc (12 0 0 0 12 0) basic clusters consisting of 1421 and 1422 bond-types, and the hcp basic cluster becomes the dominant one with decreasing temperature, the second one is mainly the fcc (12 0 0 012 0) basic clusters consisting of 1421 bond-type, and their crystallization temperatures Tc would be 1073 and 1173 K,respectively.