A superstructure can elicit versatile new properties in materials by breaking their original geometrical symmetries. It is an important topic in the layered graphene-like two-dimensional transition metal dichalcogenides, but its origin remains unclear. Using diamond-anvil cell techniques, synchrotron X-ray diffraction, X-ray absorption, and first-principles calculations, we show that the evolution from weak van der Waals bonding to Heisenberg covalent bonding between layers induces an isostructural transition in quasi-two-dimensional 1T-type VSe2 at high pressure. Furthermore, our results show that high pressure induces a novel superstructure at 15.5 GPa rather than suppresses it as it would normally, which is unexpected. It is driven by Fermi-surface nesting, enhanced by 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.