The interactions between electromagnetic field and the biological system can lead to the change of biological morphology, structure, function and other aspects at the different levels of biological targets. The domestic sewage is secondarily disinfected using continuous electromagnetic waves, the microscopic molecules have a certain dipole-moment and the biological molecular aggregates with dielectric properties of the cell may generate dielectric loss under the effect of the applied electromagnetic field. The thermal effect will be produced by putting the microwave energy into the heat of irregular movement which increases biological system's temperature. Under the influence of an applied electromagnetic field, the membrane potentially undergoes conformational changes that would affect K + ion, Na + ion channels open and make the voltage-dependant Ca 2+ ion open, the high concentration of Ca 2+ ion of the membrane into the cell along the potential gradient, which leads to cell death, resulting in the biological non-thermal effects, the greater the changes of cellular transmembrane voltage, the higher the rate of cell death. The experiment results show that the microwave secondary sterilization has a good sterilizing effect, the method has the advantages of high efficiency, low cost, simple operation, easy automation, without adding any substance and does not produce any secondary pollution, etc.