This work demonstrates the fabrication of zinc oxide-carbon nanotube (ZnO/CNT) heterostructures with tunable photocatalytic activity via microstructure modulation. The ZnO/CNT heterostructures are constructed in one-step hydrothermal procedure consisting of in situ anchoring of ZnO nanostructures with dispersible CNTs in an aqueous alkali solution containing bile salts as a dispersant. Observation via scanning (SEM) and transmission (TEM) electron microscopy reveals self-assembled heterostructures of monodispersible CNTs tightly surrounding ZnO nanostructures with multimorphology. The XRD, FT-IR, Raman and XPS analysis confirm that the CNTs were successfully incorporated into the ZnO nanostructures with strong interfacial contact of covalent bonding rather than simple mixing. A series of ZnO/CNT heterostructures, which varies according to their degree of doping with dispersible CNTs, exhibit distinct sunlight-induced photocatalytic activity onto the degradation of Rhodamine B (RhB). The superior photocatalytic performance of ZnO/CNT heterostructures originates from synergistic effects of sufficient interfacial bonding, self-assembly microstructures, and continuous conducting pathways between ZnO nanostructures and CNTs, which acquires better sunlight utilization and more efficient separation of electron-hole pair, confirmed by UV-Visible diffuse reflectance spectra as well as photocurrent and photovoltage analysis. This study also proposes a photocatalytic degradation mechanism of RhB dyes through detection of active species confirmed by electron-spin-resonance analysis.