The present invention discloses a multifunction frequency multiple particle accelerator and the method to solve the defect that the present accelerator is provided with singular energy and the beam power and working frequency are limited by singular power source. The accelerator comprises a pulse power producing unit which is used for producing N pulse signals with different powers; the N is more than or equal to 2; N microwave power producing units which can separately produce N microwaves with different energies under the control of the control signal and based on the N pulse signals; a power mixing unit which is provided with N inlets and N outlets and used for separately inputting microwaves corresponding to the N microwaves from each of the N inlets and outputting the N microwaves from each of the outlets; a particle beam producing unit which is used for producing N particle beams synchronously with the N microwaves; and an accelerating unit which utilizes N microwaves to accelerate N particle beams. With the present invention of the multifunction frequency multiple particle accelerator, various energy particle beams are alternatively output and the working frequency is high and the power can be multiplied; the present invention has broad application future in the fields of radiation imaging, radiation medicine and radiation processing.