Transition metal dichalcogenides (TMDs) have attracted wide attention due to their quasi-two-dimensional layered structure and exotic properties. Plenty of efforts have been done to modulate the interlayer stacking manner for novel states. However, as an equally important element in shaping the unique properties of TMDs, the effect of intralayer interaction is rarely revealed. Here, we report a particular case of pressure-tuned re-arrangement of intralayer atoms in distorted 1T-NbTe2, which was demonstrated to be a new type of structural phase transition in TMDs. The structural transition occurs in the pressure range of 16-20 GPa, resulting in a transformation of Nb atomic arrangement from the trimeric to dimeric structure, accompanied by a dramatic collapse of unit cell volume and lattice parameters. Simultaneously, a charge density wave (CDW) was also found to collapse during the phase transition. The strong increase in the critical fluctuations of CDW induces a significant decline in the electronic correlation and a change of charge carrier type from hole to electron in NbTe2. Our finding reveals a new mechanism of structure evolution and expands the field of pressure-induced phase transition.