The present invention discloses a preparation method of a bending resistant multilayer transparent conductive thin film. The preparation method comprises the following steps of S1 cleaning and dryinga substrate; S2 depositing a TCO film layer on the surface of the substrate via a megnetron sputtering technology; S3 adopting a spin-coating method to prepare the single-layer polystyrene micro-spheres on the surface of the TCO film layer, wherein the polystyrene micro-spheres are in rectangular array type distribution on the surface of the TCO film layer; S4 via the megnetron sputtering technology, depositing the metals between the gaps of the polystyrene micro-spheres; S5 removing the polystyrene micro-spheres by the organic solvent ultrasonic cleaning to obtain a metal layer on the surfaceof which the rectangular array type hemispheric pits are distributed; S6 via the megnetron sputtering technology, depositing the TCO film layer on the top surface of the metal layer to obtain the transparent conductive thin film. According to the present invention, by utilizing the polystyrene micro-spheres as the templates, and further sputtering the metal layer of the specific structure, the electrical conductivity and the bending resistance of a whole film system can be improved effectively, at the same time, the thickness of the TCO film layer can be reduced, the material cost is saved, and the transmittance of the whole film system is good.