The invention provides a manufacturing method of a TFT substrate and a prepared TFT substrate. According to the manufacturing method of the TFT substrate, based on the characteristic of high visible light transmittance of a transparent metal oxide semiconductor material and doping processing is performed on a transparent metal oxide semiconductor, so that a transparent metal oxide conductor can be obtained, and at the same time, an active layer and a pixel electrode are formed, and therefore, the number of the times of photo masking can be decreased, production efficiency can be improved, and production cost can be reduced; in addition, based on only one semi-transparent photo mask, exposure and etching are performed, so that a common electrode, and a stack light shielding layer formed by a light shielding layer and a transparent conductive layer can be obtained, and therefore, the number of the times of photo masking can be further decreased; and the light shielding layer is arranged at the lower part of a TFT, so that the electrical stability of the TFT will not be affected by illumination. The TFT substrate of the invention is simple in manufacturing process and low in production cost; and the light shielding layer is arranged at the lower part of the TFT, so that the electrical stability of the TFT will not be affected by illumination.