A TFT substrate and a manufacturing method thereof provided, including: depositing a metal thin film and a transparent conductive thin film on TFTs sequentially; coating a photoresist on the transparent conductive thin film, exposing and developing the photoresist via a half-tone mask to obtain a first photoresist layer and a second photoresist layer; etching the transparent conductive thin film and the metal thin film not covered by the first photoresist layer and the second photoresist layer; ashing the first photoresist layer and the second photoresist layer to remove the second photoresist layer; etching the transparent conductive thin film to expose the metal thin film not covered by the first photoresist layer; oxidizing the metal thin film to form a metal oxide thin film as a passivation layer; and stripping off the first photoresist layer to expose the metal thin film and the transparent conductive thin film as the pixel electrode.