The invention provides a TFT substrate and manufacturing method thereof. The TFT substrate comprises: base substrate, TFT layer, passivation layer and pixel electrode, stacked in above order; wherein the pixel electrode comprising: main electrode, and connection electrode connected to main electrode; the connection electrode connected to TFT layer through pixel electrode via; main electrode having a cross-like slit structure with branch electrode on four trunks of cross, and the connection electrode comprising a plurality of parallel stripe-shaped first branch electrodes, and a second branch electrode connected to the first branch electrodes; by disposing the first branch electrodes, the connection electrode having a shape similar to main electrode to make the main and connection electrodes having similar single slit diffraction when exposed to reduce or eliminate the photo-resist thickness difference in pixel electrode area in the 3M process to avoid display defect and improve yield rate.