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The van der Waals (vdW) ferromagnet Fe3-xGeTe2 has attracted much research interest as a host for magnetic skyrmions. Despite numerous investigations, identifying the origin of the Dzyaloshinskii–Moriya interaction (DMI) and achieving a controllable acquisition of the skyrmion phase in Fe3-xGeTe2 remains challenging. In this study, we comprehensively investigated the crystal structure and magnetic properties of Fe3-xGeTe2 with varying Fe concentrations. Our results revealed a pronounced Fe atom displacement that increased with decreasing Fe content. Combined with first-principles calculations, we found that this atomic displacement caused the original centrosymmetric crystal structure to transform into non-centrosymmetric symmetry, resulting in a considerable DMI. Moreover, by tuning the Fe content and sample thickness, we achieved a controllable skyrmionic phase transition from Néel-type skyrmions to Bloch-type skyrmionic bubbles. Micromagnetic simulations revealed that this transition was governed by a delicate competition between dipole–dipole interaction and the DMI. Our findings may help resolve the protracted debate on the origin of the DMI and variable skyrmionic phases in Fe3-xGeTe2, which are of great importance for exploring vdW ferromagnet-based spintronic devices.