A thin film transistor (TFT) substrate and a manufacturing method thereof are disclosed. The manufacturing method comprises: after a first metallic layer is formed on the TFT substrate, annealing the TFT substrate so that lattices of the first metallic layer are re-arranged to prevent occurrences of grain boundary defects in the first metallic layer. According to the present disclosure, after the first metallic layer is formed on the TFT substrate, the TFT substrate is annealed in sequence to re-arrange lattices of the first metallic layer. This effectively prevents occurrences of grain boundary defects and, consequently, metal protrusions in the first metallic layer.