The invention discloses a method for cultivating organic selenium-enriched rice. The method is characterized by comprising the following steps of: respectively preparing selenium-enriched seedling cultivating matrixes and selenium-enriched organic and inorganic special fertilizers by taking selenium-containing flax cakes as a selenium source, utilizing the selenium-enriched seedling cultivating matrixes in the seedling cultivation of rice, and respectively applying the selenium-enriched organic and inorganic special fertilizers as a base fertilizer and additional fertilizer before transplanting seedlings of the rice and before the farmland rest at the last phase of tillering of the rice. According to the method for cultivating the organic selenium-enriched rice, disclosed by the invention, conventional methods in which selenium-containing solution or selenium-containing leaf surface fertilizer is sprayed at a flowering phase and a seed phase of rice in the current selenium-enriched rice production or the selenium-containing solution is added in a rice processing procedure are changed, unsafe factors in the production of the selenium-enriched rice are avoided, and the production ofthe selenium-enriched rice is economical, efficient and pollution-free.