Amorphous InGaZnO (a-IGZO) TFTs become mainstream at the forefront of display backplanes and are actively expanding their area for next-generation optoelectronic devices such as flexible and transparent displays. For flexible displays, low temperature processed passivation technology is required to keep the reliability of the electrical properties in a-IGZO TFTs without damaging flexible plastic substrates. Here, we proposed a low-temperature passivation process using a dual-chamber system. A high-quality passivation layer composed of octadecyl-trichlorosilane was formed at 140 °C under vacuum on the back-channel of a-IGZO TFTs using the system. The thermally deposited self-assembled monolayers (SAMs) enable the formation of hydrophobic surfaces on a-IGZO TFTs, leading to the protection of the back-channel against water and oxygen efficiently. As a result, the electrical characteristics such as the threshold voltage shift, hysteresis, field-effect mobility, and negative bias stress of the SAM treated TFTs were significantly improved compared to those of the control TFTs.