A superstructure can elicit versatile new properties of materials by breaking their original geometrical symmetries. It is an important topic in the layered graphene-like two-dimensional transition-metal dichalcogenides (TMDs), but its origin remains unclear. Using diamond-anvil cell techniques, synchrotron x-ray diffraction, x-ray absorption, and the first-principles calculations, we show that the evolution from the weak Van der Waals bonding to the Heisenberg covalent bonding between layers induces an isostructural transition in quasi-twodimensional 1T-type VSe 2 at high pressure. Furthermore, our results show that high-pressure induce a novel superstructure at 15.5 GPa, rather than suppress as it would normally, which is unexpected. It is driven by the Fermi surface nesting, enhanced by the pressure-induced distortion. The results suggest that the superstructure not only appears in the two-dimensional structure but also can emerge in the pressure-tuned three-dimensional structure with new symmetry and develop superconductivity.