A medical proton heavy ion accelerator comprises ion sources, a low energy injector, a cyclotron and a traveling wave linear accelerator connected in sequence; the ion sources comprise a hydrogen ionsource and a carbon ion source, and can provide hydrogen ions and carbon ions, thus enabling the medical proton heavy ion accelerator to has two radiotherapy modes that include a proton ray mode and aheavy ion ray mode; said two radiotherapy modes are mutually implemented, and can be selected according to real treatment demands; the cyclotron can directly accelerate a hydrogen ion beam or a carbon ion beam from a low energy level to a high energy level, thus providing higher acceleration efficiency and effect; the energy of the proton beam or carbon ion beam emitted by the traveling wave linear accelerator can be adjusted, thus obtaining the proton beam or carbon ion beam of different energy values, satisfying different dosage demands for curing cancers, providing a strong adaptability, and improving the cancer treatment effect.