In the present work, we assessed the photocatalytic performance of the new 3-D/3-D Z-scheme heterojunction composite for the degradation of dimethyl phthalate (DMP). The composite was composed by marimo-like Bi2WO6 and mammillaria-like ZnO which was named BWZ. The composite was successfully fabricated using a hydrothermal-precipitation method and analyzed via different characterization techniques. Under natural sunlight irradiation, the optimal composite with 20 wt% of Bi2WO6/ZnO (20-BWZ) exhibited a photodegradation rate constant of 0.0259 min−1, which reached 2.3 and 5.9-folds greater than those of pure ZnO (0.0112 min−1) and Bi2WO6 (0.0044 min−1), respectively. That was predominantly attributed to the formation of a Z-scheme photocatalytic system in the as-synthesized composite reduced the charge carrier recombination and accelerated the photoactivity. Transient photocurrent response and electrochemical impedance spectroscopy analyses were performed to confirm this conclusion. The reusability test indicated that the 20-BWZ had no significant deactivation after four runs, which inferred good stability of the as-prepared composite. Furthermore, the quenching test demonstrated that the photogenerated hole, superoxide anion radical and hydroxyl radical were all involved in the photodegradation of DMP, among which •OH was the principal reactive species. This work revealed that the as-prepared BWZ composites have great potential applications for the degradation of refractory pollutants in the environmental remediation field.