A multi-energy frequency-multiplying particle accelerator and a method thereof are disclosed in order to overcome the drawbacks of the existing accelerator, such as single energy level, beam current and operating frequency limited by a single power source. The accelerator comprises a pulse power generation unit for generating N pulse signals with different power levels, N is equal to or greater than 2; N microwave power generation units for, under the control of a control signal, generating N microwaves with different energy levels based on said N pulse signals, respectively; a power mixing unit having N entrances and one exit and for inputting a corresponding microwave among said N microwaves from each of said N entrances and outputting said N microwaves from said one exit; a particle beam generation unit for generating N particle beams in synchronization with said N is microwaves; and an accelerating unit for using said N microwaves to accelerate said N particle beams, respectively. Since the multi-energy frequency-multiplying particle accelerator of the present invention can output alternately particle beams of different energy levels and thus has improved operating frequency and multiplied power, it will find a wider application prospect in the field of radiograph imaging, radioactive medicine and radiation processing industry.