The invention relates to the technical field of an ion acceleration method in a proton-heavy ion cancer-treating synchrotron, in particular to a synchronous acceleration method of high frequency variable harmonics and a control device thereof. In the invention, the control device corresponding to the synchronous acceleration of the high frequency variable harmonics is used; a high frequency cavityin a synchrotron is adopted to use a high-frequency electric field of high-order harmonics (second harmonic or fourth harmonic) to accelerate ions, and the frequency of the high-order harmonics is equal to cyclotron frequency of storing ions; when ions are accelerated to a certain amount of intermediate energy, high frequency electric field frequency of the high frequency cavity is changed into low-order harmonics (first harmonic or second harmonic) of the cyclotron frequency of the storing ions; and the ions are accelerated continuously until the ion energy thereof can satisfy the clinical requirements. In work frequency range of the high frequency cavity, high frequency variable harmonics acceleration technology is used, so that difficulty in low end extension is avoided when ferrite isloaded with high frequency system bandwidth. The invention can broaden the energy range of capturing and accelerating ions, and realizes the requirement of ion beam irradiation therapy of tumor of human body with different depths on beam energy on the basis of narrower work frequency range of the high frequency cavity.