Molybdenum sulfide (MoSx) has recently emerged as a promising catalyst for the hydrogen evolution reaction (HER) in water splitting that may replace the noble metal, such as platinum, as a cost-effective and high catalytic materials. It has been reported that two-dimensional structured MoSx exhibit significant amount of exposed S-edge, which can be an active electrocatalytic catalyst for hydrogen production. However, the current reports mainly focusing on the planar electrode, where the catalyst utilization and the number of active sites are limited due to the lower exposed specific surface area (SSA) of supporting electrodes. In this work, we utilize the freeze-drying method to produce a porous three-dimensional (3D) structure assembled by graphene flakes. The as-prepared 3D graphene scaffold shows high surface area, high porosity while low density, which makes it as an ideal conductive electrode for supporting of MoSx catalysts. Moreover, it was found out that the crystallinity of MoSx, controlled by thermolysis temperature of thiosalts precursor ((NH4)2MoS4), shows significantly influence the performance of HER. The optimized annealing temperature for the designed hybrid electrodes (MoSx/3D-graphene) was found to create a lot of active sites, which facilitate the electrocatalytic performance for water splitting (overpotential of 163 mV @10 mA/cm2 and a Tafel slope of 41 mV/dec). The study provides a potential material, which could pave the way for future applications of hydrogen energy.