The paper aims to solve the problem that inorganic oxide high barrier packing materials prepared by physical sputtering deposition are not flexible enough and likely to crack during service process. ZnO/PI/PET composite films were prepared on the PET plastic surface by RF magnetron sputtering with zinc oxide (ZnO) and polyimide (PI) as target materials. Herein, the influence of the introduction of PI on the microstructure and performance of ZnO barrier layer was analyzed in detail, the preparation process of ZnO/PI was optimized as well. The micromorphology and packing properties of the composite films were greatly influenced by the sputtering power density ratio (PZnO/PPI). With the decrease of PZnO/PPI, and PI content deposited increased, the shape of ZnO nanoparticles gradually changed from squeezed oatmeal to spherical nanoparticles, and the ball diameter size showed a decreasing trend. In addition, the flexibility of the sedimentary layer increased significantly. After 100 circles of folding, no obvious cracks were found (PZnO/PPI≤2). When the PZnO/PPI was 2, the argon flow rate was 40 mL/min, the deposition time was 30 min, and the working pressure was 0.5 Pa, the ZnO/PI/PET composite barrier film showed the best barrier capacity, with water vapor transmittance rate (WVTR) of 0.342 g/(m2∙d) and oxygen transmittance rate (OTR) of 0.365 mL/(m2∙d). Therefore, the introduction of proper amount PI fragment can effectively improve the flexibility and folding resistance of inorganic oxide barrier layer, and further improve the barrier ability of composite deposition film to small gas molecules such as water vapor and oxygen.