A superconducting magnet system and a cyclotron using the same. The superconducting magnet system includes a cryogenic device, a superconducting device and a protecting module. The cryogenic device includes a refrigerating machine and a cryogenic container assembly. The cryogenic container assembly includes a first container end, a connecting tube and a second container end. The first container end is communicated with the second container end through the connecting tube. The superconducting device includes a superconducting coil arranged in the first container end and immersed in a liquid or gaseous cooling medium. The protecting module is connected to the superconducting coil and is configured to protect the superconducting coil if the superconducting coil suffers a quench.