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Plasma‐assisted epitaxially grown silicon (plasma‐epi Si) is a new silicon‐based material with a tailorable nanostructure. Nanovoids can be introduced into plasma‐epi Si during growth, enabling the bottom‐up fabrication of porous Si for applications such as batteries, hydrogen storage, and even explosives. To fully control the nanostructure of plasma‐epi Si, its growth dynamics must be studied. In this study, the correlation between hydrogen incorporation and defect nanostructures in plasma‐epi Si grown under various process conditions is investigated, and the experimental results are supported by molecular dynamics simulations. The nanostructural evolution during growth suggests a model in which plasma‐epi Si shows two growth stages distinguished by different dominant defect nanostructures. In the initial growth stage, the nanostructure can be controlled by the deposition conditions, whereas the nanostructure is dominated by interconnected voids, forming a porous structure. In the subsequent bulk growth stage, the material growth is less sensitive to the deposition conditions, whereas the nanostructure becomes prevalent isolated defects. In the results of this study, different strategies for the plasma‐epi Si growth process for different applications are suggested. In these results, a better understanding of this new material may be provided and the discovery of various applications for bottom‐up‐grown porous Si is facilitated.