A organic fertilizer for controlling pollution or accumulation of heavy metal cadmium in rice and a preparation method and an application method thereof are related to the technical field of fertilizers. The fertilizer is, based on 100 kg of organic material with a water content of 15%, added with 0.05-5 kg of iron salt calculated as iron, and is also added with manganese salt, zinc salt and copper salt, wherein a mass ratio of the iron salt calculated as iron, the manganese salt calculated as manganese, the zinc salt calculated as zinc and the copper salt calculated as copper is 1:0.2-8:0.08-2:0.001-0.5.