Two-dimensional transition-metal dichalcogenide nanosheets made of MoS2 are widely studied owing to their applications as electrocatalysts and electrode materials. To specify key design parameters for optimizing catalytic performance of MoS2, we developed a soft-chemical lattice manipulation strategy to precisely tune their structural, defect, and morphological characteristics via self-assembly of the exfoliated MoS2 nanosheet with various guest cations. Most alkali-metal-restacked MoS2 nanosheets exhibit a layer-by-layer ordered intercalation structure containing water monolayers; however, self-assembly with Li+ ions led to the intercalation of thicker water bilayers, attributed to the higher hydration energy of smaller Li+ ions. Increasing the basal spacing induced a gradual phase transformation from 2H-type bulk MoS2 to 1T MoS2 structure restacked with H+ and Na+ ions and further to a highly distorted 1T′ MoS2 structure restacked with Li+ and Cs+ ions. Additionally, an increase in the guest size led to an increase in the defect concentration. The Cs+-restacked MoS2 exhibited the lowest overpotential and smallest Tafel slope for hydrogen evolution reactions. Correlating the electrocatalytic activity with structural, defect, and morphological parameters revealed that unlike interlayer spacing and crystal phase, the surface area and defect concentration are dominant factors governing the electrocatalytic performance of MoS2. This conclusion was supported by in situ Raman analysis, which indicated enhanced hydrogen adsorption and accumulation on the Cs+-restacked MoS2 surface, suggesting an efficient Volmer–Tafel reaction pathway.