Effective separation of charge and high cycle stability are key factors for photocatalyst application. In this paper, the spatially separated Pt/CdS/N–ZnO/CoOx graphene microtubule (PCNZCo-GM) is prepared by a capillary action assisted hydrothermal method for enhancing charge separation efficiency and photocatalytic oxidation ability. In the spatially separated composite, Pt as an electron collector and CoOx as a hole collector were selectively decorated on the inner and outer surfaces of the CdS/N–ZnO graphene microtubule, which prompts photogenerated electrons and holes near the surface to move in the opposite direction. N–ZnO possesses a wider light absorption range, and the construction of a Z-scheme heterojunction between CdS and N–ZnO can effectively promote the charge separation. The graphene microtubule structure with an oxidation–reduction cocatalyst supported on its inner and outer surfaces is conducive to charge separation, reusability and mass transfer in photocatalytic processes. The PCNZCo-GM composite photocatalyst displays a remarkable photocatalytic oxidation efficiency for methyl orange (MO, 93% removal efficiency in 60 min) and an excellent bacterial inactivation rate of almost 100% under 60 min of illumination. Based on the macroscopic appearance and preferable mechanical strength of the 3D graphene microtubule, the PCNZCo-GM composite possesses high cycle stability in photocatalytic processes and its excellent photocatalytic performance was well maintained after five applications.