The invention provides a BCE TFT substrate and manufacturing method thereof. The method uses low deposition power and low oxygen content to deposit first silicon oxide thin film; then increases deposition power with low oxygen content to deposit second silicon oxide thin film. The first and second silicon oxide thin films form a passivation layer; the second silicon oxide film is implanted with oxygen to form a superficial layer so that the Si:O atomic ratio in the superficial layer is close to or same as Si:O atomic ratio of SiO2, to ensure the passivation layer in contact with the air side is strongly hydrophobic to prevent outside water vapor into the back-channel, while ensuring the side of passivation layer contacting IGZO active layer has a lower oxygen content to reduce the probability of forming unbalanced O-ions at the interface between passivation layer and IGZO active layer.