The invention discloses a proton therapy system based on a compact superconducting cyclotron. The proton therapy system includes a superconducting cyclotron system, an energy selection system and a beam transportation system, a fixed treatment room subsystem and a rotary frame treatment subsystem; the fixed energy proton beam led out by the superconducting cyclotron in the superconducting cyclotron system can be a continuously adjusting proton beam of 70-200MeV via the energy selection system, so that the longitudinal adjustment of the range during the proton therapy of tumors can be met; thebeam is transmitted to the fixed treatment room subsystem and the rotary frame treatment subsystem via the beam transportation system; the superconducting cyclotron system, the energy selection system, the beam transportation system and a treatment head are subjected to cooperative control to realize the transverse expansion of the proton beam, so that the intensity modulation treatment of the tumor can be completed. According to the invention, the innovation is good, the practicability is high, the beam intensity of the superconducting cyclotron is adjustable, and the intensity modulation treatment can be realized; and the system has an extremely important promotion effect on the accuracy, effectiveness and high efficiency of tumor treatment of a patient.