We have demonstrated that the island nucleation in the initial stage of epitaxial thin film growth can be tuned by substrate surface charge doping. This charge effect was investigated using spin density functional theory calculation in Fe-deposition on graphene substrate as an example. It was found that hole-doping can apparently increase both Fe-adatom diffusion barrier and Fe inter-adatom repulsion energy occurring at intermediate separation, whereas electron-doping can decrease Fe-adatom diffusion barrier but only slightly modify inter-adatom repulsion energy. Further kinetic Monte Carlo simulation showed that the nucleation island density can be increased up to ten times larger under hole-doping and can be decreased down to ten times smaller than that without doping. Our findings indicates a new route to tailoring the growth morphology of magnetic metal nanostructure for spintronics applications via surface charge doping.