The invention discloses a fertilizer composition for preventing and controlling slight and medium cadmium contamination in a rice field and an application manner thereof, belonging to the field of fertilizer. The fertilizer composition comprises macroelement fertilizer used for preventing and controlling cadmium absorption of rice grains, medium-element fertilizer used for inhibiting conjugation of elemental cadmium and transport proteins in rice, and a soil amendment used for reducing transfer of elemental cadmium from soil and rice straw to rice grains. According to the invention, the macroelement fertilizer, the medium-element fertilizer and the soil amendment are used for guaranteeing safe production of rice in cadmium-contaminated soil in three aspects, i.e., the activity of elemental cadmium, the content of cadmium in soil and migration of cadmium in rice; so the prepared fertilizer composition is good in effect, low in cost and easy to apply and produces substantial economic benefits.