The invention discloses a method for detoxification of citrus by utilizing microwaves, and belongs to the technical field of microwave application. The method is characterized in that during microwave pretreatment, the microwave irradiation frequency is 1.0 GHz-3.0 GHz, the power is 100-900 W, the microwave irradiation time is 5-20 seconds, then pausing is carried out for 10-30 seconds, repetitive operation is carried out 3-10 times, the temperature of each part of the citrus is increased to 40-45 DEG C, and the constant temperature is maintained for 30-60 seconds; then it is adjusted that the microwave irradiation frequency is 350 MHz-950 MHz, the power is 1,000-3,000 W, the microwave irradiation time is 3-10 seconds, then pausing is carried out for 20-60 seconds, repetitive operation is carried out 5-20 times, the temperature of each part of the citrus is increased to 50-55 DEG C, the constant temperature is maintained for 1-5 minutes, and citrus detoxification is carried out by utilizing the microwaves. The method for detoxification of the citrus by utilizing the microwaves can make each part of the citrus reach the fatal temperature of candidatus liberibacter more quickly and evenly, and a tree body is not affected; under the non-thermal effect of a microwave electromagnetic field, nucleic acid, protein and other molecules in the candidatus liberibacter are easy to denature and inactivate to achieve double sterilization effects; the detoxificated citrus through the microwaves are detected by adopting GB/T 28062-2011 , and the negative conversion ratio of the candidatus liberibacter is greater than or equal to 82%. The method is an efficient, quick and environment-friendly citrus detoxification method.