Fabricating high-quality thin films on a 3D structured polymer substrate is crucial in realizing high-performance flexible electronics. Herein, simple yet effective twofold strategies are demonstrated to directly fabricate flexible thin film capacitors on polymer substrate: the crystallization of high-k TiO2 film by plasma-assisted atomic layer annealing at low temperature (80 °C) on nanostructured polycarbonate (PC) substrates fabricated by simple dynamic nanoinscribing (DNI) technique. Plasma-induced amorphous-to-anatase phase transformation occurs in PEALD TiO2/ZrO2 bilayer thin films, resulting in the capacitance density increase by 30%. The DNI patterning of PC substrates in two directions further increases the surface area by 35% and the capacitance density by 37%, leading to the flexible capacitor of a record-high capacitance density (24.2 nF mm−2) with mechanical stability.