Based on first-principles simulations, we revisit the crystal structures, electronic structures, and structural stabilityof the layered transition metal dichalcogenides (TMDCs) NbS2, and shed more light on the crucial roles of the van der Waals (vdW) interactions. Theoretically calculated results imply that the vdW corrections are important to reproduce the layered crystal structure, which is significant to correctly describe the electronic structure of NbS2. More interestingly, under hydrostatic pressure or tensile strain in ab plane, an isostructural phase transition from two-dimensional layered structure to three-dimensional bulk in the I4/mmm phase has been uncovered. The abnormal structural transition is closely related to the electronic structure instability and interlayer bonding effects. The interlayer Nb-S distances collapse and the interlayer vdW interactions disappear, concomitant with new covalent bond emerging and increasing coordination number. Present work highlights the significance of the vdW interactions, and provides new insights on the unconventional structural transitions in NbS2, which will attract wide audience working in the hectic field of TMDCs.