A color filter substrate includes a substrate, a light-shielding layer, a color filter layer, at least one padding structure, a passivation layer, a transparent conductive layer and at least one spacer. The substrate has a light-shielding region and pixel regions. The light-shielding layer is located in the light-shielding region. The color filter layer is located in the pixel regions. The padding structure disposed on the light-shielding layer and the color filter layer are in the same layer. The passivation layer covers the padding structure, a portion of the light-shielding layer and the color filter layer. The spacer is disposed on the transparent conductive layer which covers the passivation layer and located above the color filter layer. A height of the spacer and a thickness of the color filter layer in total are less than a height of the padding structure and a thickness of the light-shielding layer in total.