<p>Dimensionality and magnetic anisotropy jointly determine whether long-range magnetic order survives in low-dimensional magnets. Although theory predicts that perpendicular magnetic anisotropy can stabilize ferromagnetism in two-dimensional systems, an experimental realization of a continuous crossover from a three-dimensional Heisenberg-type system to a two-dimensional Ising-type ferromagnet has remained challenging. Here we demonstrate such a crossover in thin layers of the van der Waals ferromagnet Fe₃GeTe₂. Counterintuitively, the monolayer—one quintuple layer, where no van der Waals gap exists—exhibits three-dimensional Heisenberg-like behaviour. We reveal that this arises from substantial structural modifications relative to bulk-like quintuple layers. Bilayers and thicker films revert to the bulk-like structure, which, together with substantial self-intercalation of Fe in the van der Waals gaps, stabilizes perpendicular magnetic anisotropy and drives the system into a two-dimensional Ising-like regime. Our findings emphasize the critical role of self-intercalation and provide insights into how subtle atomic-scale structural evolution, rather than nominal thickness alone, governs magnetic ordering in low-dimensional materials.</p>