•CNC, ZnO/CuO and hybrid CNC/ZnO/CuO nanostructures were synthesized and characterized.•Nanostructures were characterized by TEM, SEM, EDX, XRD, FT-IR and XPS.•Hybrid nanostructure exhibited higher photocatalytic activity towards dye degradation.•Hybrid CNC/ZnO/CuO nanostructure have greater antibacterial and larvicidal activities.•Hybrid nanostructure achieved better larvicidal activity against malaria vector.•Integrating CNC into nanostructures has increased its activities. Cellulose nanocrystal (CNC) and ZnO/CuO nanostructure were successfully synthesized by acid hydrolysis and sol-chemical methods, respectively. For the first time, CNC was used as a host polymer for synthesis of CNC/ZnO/CuO through In-situ solution casting technique. Morphological and structural of CNC, ZnO/CuO and hybrid CNC/ZnO/CuO were investigated by TEM, SEM-EDX, FT-IR, XRD and XPS analyses. The analysis revealed that, poly-dispersed, smooth and rod like CNC with an average length of ∼ 85.4 nm, average diameter of ∼13.9 nm and surface charge of 0.01 mmol/gm. As well, irregular shapes as hexagonal, spherical and cluster or star like of ZnO/CuO were formed. EDX and XRD spectra exhibited highly purified CNC/ZnO/CuO and pointed to cellulose II crystallite form with a monoclinic structure. The results demonstrated that, 91.3 % and 99.7 % dye degradation was achieved after 40 min of irradiation due to ZnO/CuO and CNC/ZnO/CuO treatment. Moreover, the inhibition zones formed due to 100 ppm ZnO/CuO were duplicated after integrating CNC (from 7.7:10.3 mm to 14.3:20.3 mm). The hybrid nanostructure exhibit larvicidal activity against Anopheles stephensi better than CNC and ZnO/CuO nanostructures.