With their tunable electronic structure, transition metal dichalcogenides offer a high surface area and enhanced active sites, making them a promising electrocatalyst for hydrogen production techniques. However, restacking of 2D layers and particle aggregation during material preparation negate its advantages. Herein, we developed a flower-like morphology with numerous molybdenum disulfide (1T/2H MoS2) nanosheet petals. The final formation and arrangements of MoS2 were validated through three distinct approaches: air (AD-M), vacuum (VD-M), and freeze-drying (FD-M). Interestingly, the drying phenomenon effectively alters the stacking and aggregation between the flower petals in the MoS2 and the electrocatalytic activity. Among the different drying processes, the FD-M exhibits minimal stacking and agglomeration between the nanoflowers. The FD-M exhibits remarkable catalytic activity in 1 M KOH for HER, reaching 10 mA cm−2 at a low overpotential (η10) of 198 mV and a small Tafel slope of 58.5 mV dec−1, which is lower than the AD-M (228 mV) and VD-M (215 mV). The FD process modulates the electronic structure of MoS2 by lowering stacking between layers, which effectively increases the ECSA and boosts the HER performance.