The present invention provides a manufacture method of a TFT array substrate and a TFT array substrate structure, and the TFT array substrate structure comprises a substrate (1), a first metal electrode (2) on the substrate (1), a gate isolation layer (3) positioned on the substrate (1) and completely covering the first metal electrode (2), an island shaped semiconductor layer (4) on the gate isolation layer (3), a second metal electrode (6) on the gate isolation layer (3) and the island shaped semiconductor layer (4), a protecting layer (8) on the second metal electrode (6), a color resist layer (7) on the protecting layer (8), a protecting layer (12) on the color resist layer (7) and a first pixel electrode layer (9) on the protecting layer (12); a via (81) is formed on the protecting layer (8), the color resist layer (7) and the protecting layer (12), and an organic material layer (10) fills the inside of the via (81).