The electrochemical applications of traditional carbon nanomaterials such as carbon nanotubes (CNTs) and graphene (G) powders are significantly impeded by their poor three-dimensional (3D) conductivity and lack of hierarchical porous structure. Here, we have constructed a 3D highly conductive CNTs networks and further combined it with mesoporous carbon (mC) for the creation of a core shell structured (CNT@mC) composite sponge that featured 3D conductivity and hierarchical porous structure. In the composite sponge, interconnected CNTs efficiently eliminates the contact resistance and the hierarchical pores significantly facilitate the mass transport. The electron transfer rates, electroactive surface area and catalytic activity of the CNT@mC composite sponge based catalysts were tested in the direct methanol fuel cells (DMFCs) and electrochemical sensors. In DMFCs, the Pd nanoparticles deposited CNT@mC showed significantly improved catalytic activity and methanol oxidization current. As for amperometric sensing of endocrine disrupting compounds (EDCs), CNT@mC-based catalyst gave a liner range from 10 nM to 1 mM for bisphenol A (BPA) detection and showed great promise for simultaneous detection of multiple EDCs. BPA recovery from environmental water further indicated the potential practical applications of the sensor for BPA detection. Finally, the electrochemical performance of CNT@mC were also investigated in impedimetric sensors. Good selectivity was obtained in impedimetric sensing of BPA and the detection limit was measured to be 0.3 nM. This study highlighted the exceptional electrochemical properties of the CNT@mC composite sponge enabled by its 3D conductivity and hierarchical porous structure. The strategy described may further pave a way for the creation of novel functional materials through integrating multiple superior properties into a single nanostructure for future clean energy technologies and environmental monitoring systems.