The transparent Cu2O film/Zn3In2S6 QDs/TiO2 orderly nanoarrays pn junction has been prepared via a continuous hydrothermal-co-precipitation-sputtering method. As revealed, the as-prepared Cu2O/Zn3In2S6 QDs/TiO2 transparent pn junction (Cu2O/ZIS-3-TiO2) exhibits highly transmittance of ∼85%, obvious photovoltaic conversion enhancement of ∼1.2 × 103 folds (IPCE of 1.17%) than intrinsic Cu2O/TiO2 pn junction, and decent stability during 40000s′ continuous cycle, which can be mainly ascribed to that, the Zn3In2S6 QDs with appropriate Fermi level, high quantum yields and wide band gap, can optimize the photo-generated carrier concentration-mobility kinetic equilibrium efficiently, while maintaining a high transparency. Additionally, TiO2 orderly nanoarrays can provide carrier transportation pathway, increase solar efficiency and physical stability.