With the high energy ball milling method, a Co9S8-decorated reduced graphene oxide (RGO) composite, which shows excellent hydrogen storage capacity, has been successfully fabricated with a well-organized layered structure. Moreover, the stabilized mechanism of the well-organized layered structure is investigated and attributed to the strong interactions between Co9S8 and defective RGO. The C-S bond interaction is identified and the hydrogen storage process is also studied with different analysis methods. Finally, an optimized Co9S8 to RGO weight ratio of 6:1 shows excellent electrochemical performances in terms of the excellent cycling stability and competitive hydrogen storage capacity of 4.86 wt%.