Rational synthesis of a hierarchical porous architecture with highly active and consecutive conductive network is very critical to achieve the high-performance of nanomaterials in electrochemical energy conversion and storage. We propose here a hierarchical micro-/nanostructured hybrids constructed by the dual carbon shell nanowire host containing CoP nanocrystals of several nanometers, which generates Co-based metal-organic framework on graphene oxide nanosheets in situ and followed a direct phosphorization (CoP@NC/rGO). The dual carbon shell, consisting of Co-based metal-organic framework derived porous doped carbon (NC) and reduced graphene oxide (rGO), can not only impedes CoP nanocrystals from coalescing, and renders highly exposed the electrochemically accessible active sites, but also provides the multidimensional pathways for rapid electron and ion transportation. More importantly, the covered dual carbon shell on CoP nanocrystals plays a role as a protective layer to impede the nanocrystals' corrosion. By virtue of compositional and structural advantages, the micro-/nanostructured CoP@NC/rGO hybrids manifest outstanding energy storage properties when evaluated as anodes for lithium/sodium ion batteries. Remarkably, it also reveals highly efficient electrocatalytic performance for hydrogen evolution reaction in acid media with low Tafel slope, overpotential and robust durability.