Nanodiamond films were deposited on Si substrate by introducing a time dependent on/off modulation of $CH_4;and;O_2$ flows in a vertical-type microwave plasma enhanced chemical vapor deposition system. Surface morphology and diamond quality of the film were investigated as a function of the on/off modulation time interval. The diamond nucleation density on the substrate was enhanced under low temperature and low pressure condition. In addition, the diamond nucleation density was enhanced by increasing the on/off modulation time interval. Enhanced diamond quality was noticeable under the condition of a longer on/off modulation time interval. It was suggested that the nanodiamond nuclei formed the cluster formation.