The invention discloses a controlled-release carbon source material for repairing polluted underground water organisms and a preparation method thereof and belongs to the field of underground water repairing. The controlled-release carbon source material comprises a core and a shell wrapping the core, wherein the core comprises the following components in percentage by weight: 40 to 86 percent ofcarbon releasing raw material, 1 to 25 percent of nutritional raw material, 5 to 45 percent of plastic bonding raw material, 5 to 20 percent of high-permeability raw material and the balance of water; the shell comprises the following components in percentage by weight: 10 to 40 percent of carbon releasing raw material, 1 to 10 percent of nutritional raw material, 20 to 80 percent of plastic bonding raw material, 0 to 40 percent of high-permeability raw material and the balance of water; and the controlled-release carbon source material is prepared by a compound formula consisting of the carbon releasing raw materials, nutritional elements and multi-component inorganic combined raw materials. The controlled-release carbon source material meets a microbial nutrition demand and requirementsfor long-time stable material supply during underground water repairing, certain mechanism strength and uniform sphericity; furthermore, the defects of high carbon loss, uncontrollable releasing rateand the like in the conventional carbon source compensation method are overcome; and the continuity of the underground water organism repairing effect is realized.