The growth of well-ordered Mn nanodots arrays on Si(111)-7×7 reconstructed surface was investigated by means of scanning tunneling microscopy (STM) as well as Kinetic Monte Carlo (KMC) simulation. Mn atoms deposited slowly onto elevated substrates were observed to occupy preferentially on the faulted half unit cells (FHUCs) of Si(111)-7×7 surface. The preference occupancy in the FHUCs, P F , defined as the ratio of number of FHUCs occupied by Mn nanodots to number of all occupied in two halves, decreases with increasing deposition rate as well as decreasing substrate temperature. The KMC simulations, which are in good agreement with the experimental results, were employed to optimize the growth conditions, including deposition rate and substrate temperature, for the self-organized growth of Mn nanodots arrays on Si(111)-7×7 reconstructed surface. By adjusting the deposition rate, one can control the growth of well-ordered and uniform Mn nanodots arrays to form either a triangular symmetry or a honeycomb one.