The invention discloses a vacuum suction cup isolation type automatic anti-ice device and method of a low-temperature filling system. The device comprises a suction cup (3). A tray (5) and elastic supporting plates (4) are fixed to the suction cup (3). A sliding shaft (15) is fixedly arranged on the tray and is mounted in a base (10) in a sleeved manner. A proximity switch (14) and an induction block (9) are fixedly arranged on the base and the sliding shaft correspondingly. An air suction hole connector (7), an air inlet hole connector (8) and a pressure sensor (6) are arranged on the tray. The method comprises the following steps that the device is aligned to and approaches to the low-temperature filling system, after the device is in contact with the low-temperature filling system, a spring is compressed, and the device stops propulsion; negative pressure is formed in the suction cup; and the device is adsorbed to the low-temperature filling system, and the anti-ice function is achieved. The vacuum suction cup isolation type automatic anti-ice device and method of the low-temperature filling system have the beneficial effects of being good in anti-ice good, high in adaptability, high in universality, high in automation degree, safe to use and the like.