The process of diamond nucleation by hot filament chemical vapor deposition was investigated by atomic force microscopy. It was observed that a large number of micro-defects (pits) were produced on the surface of the silicon substrate due to ion bombardment under the negative potential and diamond nucleated on the pits. The formation of the pits and their role in diamond nucleation were theoretically approached. The results indicate that the number of the pits increased with increasing potential, the diamond nucleation density and the nucleation rate were functions of the pits, and they were in agreement with the experiment results.