The invention relates to a method for culturing submerged plant seeds. The method comprises the following steps: A, soaking the submerged plant seeds produced by apomixia in 0.01-1wt% of dimethoate or sodium hypochlorite solution for 1-6 hours, washing the soaked submerged plant seeds with clear water, naturally drying the soaked submerged plant seeds in the air; B, standing the submerged plant seeds at 20-25 DEG C for 1-3 days, storing at 1-5 DEG C for 1-2 days, and preserving at 30-40 DEG C for 12-36 hours; C, soaking the submerged plant seeds in solution containing plant hormone, trace elements and inorganic salt for 12-24 hours; and D, burying the submerged plant seeds in a matrix by a depth of 3-5cm, and then putting the matrix in which the submerged plant seeds are buried at the bottom of river or lake water. The matrix comprises humus, sediment at the bottom of river and lake, bank soil, clay and sand. The submerged plant seeds bred by the method have high germination rate and environmental adaptability.