The effect of pretreatment bias on the nucleation and growth mechanisms of the ultrananocrystalline diamond (UNCD) films on the Si substrate via bias-enhanced nucleation and bias-enhanced growth (BEN-BEG) was investigated using cross-sectional high-resolution transmission electron microscopy, chemical bonding mapping, and Raman spectroscopy. The mirror-polished substrate surface showed the formation of a triangular profile produced by a dominant physical sputtering mechanism induced by ion bombardment of ions from the hydrogen plasma accelerated toward the substrate due to biasing and a potential hydrogen-induced chemical reaction component before synthesizing the UNCD films. The BEN-BEG UNCD films grown on the Si substrate with biased and unbiased pretreatments in the hydrogen plasma were compared. In the case of the bias-pretreated substrate, the SiC phases were formed at the peaks of the Si surface triangular profile due to the active unsaturated Si bond and the enhanced local electrical field. The UNCD grains grew preferentially at the peaks of the triangular substrate surface profile and rapidly covered the amorphous carbon (a-C) and oriented graphite phases formed in the valley of the surface profile. In the case of the substrate with unbiased pretreatment, the SiC phases were formed via the reactions between the hydrocarbon species and the active Si atoms released from the substrate with assistance of the hydrogen plasma. The UNCD grains nucleated on the nucleating sites consisting of the SiC, a-C, and graphite phases. Growth mechanisms for the BEN-BEG UNCD films on both Si substrates were proposed to elucidate the different nucleation processes. Applying bias on the Si substrate pretreated in the hydrogen plasma optimized the nucleation sites for growth of UNCD grains, resulting in the low content of the nondiamond phases in UNCD films.