The present invention provides an ESL TFT substrate structure and a manufacturing method thereof. In the ESL TFT substrate structure, an etch stop layer (5) includes a first via (51) and a second via (52) formed therein to correspond to two side portions of an oxide semiconductor layer (4). A drain terminal (6) is set in engagement with the oxide semiconductor layer (4) through the first via (51). A passivation protection layer (7) includes a through hole (72) formed therein to extend to and communicate with the second via (52). An electrode layer (8) is formed on the passivation protection layer (7) and has a side portion that is adjacent to the drain terminal (6) and is set in engagement with the oxide semiconductor layer (4) through the through hole (72) and the second via (52) to form a source terminal (81) and an opposite side portion that is extended in a direction away from the drain terminal (6) to form a pixel electrode (82). The ESL TFT substrate structure has a reduced channel length so as to provide the TFT with excellent electrical conduction performance and also to reduce the size of the TFT thereby increasing an aperture ratio of pixels and reducing difficult of pixel design.