The article examines the effect of atomic number, temperature and tempering time on microstructure and mechanical of Ni bulk by molecular dynamics simulation and deformation z-axis. Samples Ni with N = 4000, 5324, 6912, and 8788 atoms at 300 K, 6912 atoms at T = 1100, 900, 700, 500, 300 K and 6912 atoms at 900 K after different annealing time. The samples were incubated with the same heating rate
. Combined with common neighborhood analysis method shown in sample is always existing four types structure: FCC, HCP, BCC, and Amor. In particular, structural units FCC, HCP and Amor always prevail and BCC are very small and appear only at 300, 500 K with 6912 atoms. When increasing atomic number, lowering temperature or increasing tempering time will facilitate crystallization process leading to increased FCC and HCP units number. The increasing FCC, HCP units number and additional appearance BCC structure led to change microstructure and mechanical of material: When increasing atom, lowering temperature and increasing incubation time lead to an increase in density of atoms that increase mechanical properties of the material.