In this paper, the effects of the quantum yield of free radicals in cryptochrome exposed to different electromagnetic fields were studied through the quantum biology. The results showed that the spikes characteristics was produced in the free radicals in cryptochrome, when it exposed to the applied magnetic field (ω = 50 Hz, B0 = 50 μT). The spikes produced by the electromagnetic field was independent of the changes of polar θ. When the frequency of the magnetic field increased, the spikes characteristics produced in unit time also increased. These results showed that the environmental electromagnetic field could affect the response of organisms to the geomagnetic field by influencing the quantum yield in the mechanism of free radical pair.It provided a basis for studying the influence of environmental electromagnetic field on biology, especially the navigation of biological magnetism.