The invention discloses a substrate improving material for a high-organic-matter bottom mud shallow lake and a preparation method thereof, and a repairing method; the substrate improving material is composed of clay, kaolin, environmental-protection ceramic filter balls and calcium peroxide. The preparation method comprises the steps: 1) selecting the clay, kaolin, environmental-protection ceramic filter balls and calcium peroxide as raw materials; 2) placing the environmental-protection ceramic filter balls in dilute hydrochloric acid, soaking, washing with clear water to be neutral, and drying; and 3) mixing evenly the clay, the kaolin, calcium peroxide and the processed ceramic filter balls according to a certain proportion, to prepare the substrate improving material. The repairing method comprises the steps: A) bamboo sticks are arranged in a lake bottom substrate improved region; B) the substrate improving material is sprinkled to the bottom of the lake from the surface of the lake; and C) submerged plants are planted on the substrate improved region, and the submerged plants are managed and maintained. The method is easy to implement and simple to operate, effectively solves the problems that the submerged plants are difficult to fixedly plant and ecological restoration projects are difficult to implement in a soft-surface high-organic-matter bottom mud lake, and accelerates the recovery of a lake ecosystem.