The invention discloses a flexible transparent thin-film electrode and a manufacturing method thereof. The structure of the electrode is characterized in that a poly (3,4-ethylenedioxythiophene) : poly (styrene sulfonate) (PEDOT:PSSY) stretchable substrate is employed. The substrate is made from a high-elasticity stretchable plastic material like a PVA material, a PDMS material, a PUA material, or a hydrogel. In addition, the manufacturing method comprises: a PEDOT:PSSY solution is deposited on an elastic plastic substrate by means of spinning, spraying, silk-screen printing or ink-jet printing. Therefore, the manufactured transparent electrode has excellent integrated performances including high transparency, high electrical conductivity, excellent electrochemical performance, high flexibility like random bending or warping, surface smoothness, and high chemical stability and the like.