Diamond films were deposited on 10.0$ imes$10.0$mm^2$ pretreated (100) Si substrate using $CH_4$, $H_2$ and $O_2$ source gases in a horizontal-type microwave plasma enhanced chemical vapor deposition system. We introduced a cyclic on/off modulation of $CH_4$ and/or $O_2$ flows is a function of the reaction time during the initial deposition stage. Surface morphology and diamond quality of the films were investigated as a function of the different cyclic modulation process of the source gases flows: For the enhancement of the nucleation density, there is an optimal process for the incorporation of oxygen. Diamond qualities of the films were improved by introducing oxygen gas during the initial deposition stage.