The invention discloses microorganism-based crack depth-width three-dimensional self-repairing concrete and a preparation method thereof. The concrete is prepared from 30-120 parts of a microbial self-repairing agent, 0-50 parts of probiotics-loaded expanded perlite, 0-50 parts of an oxygen slow-release agent, 0-50 parts of nutrient-loaded expanded perlite, 23 parts of expanded perlite with the particle size of 120 mesh, 350-500 parts of cement, 1000-1300 parts of pebbles, 400-600 parts of sand, 30-50 parts of silica fume, 2-4 parts of polypropylene fiber, 4-6 parts of a water reducer and 250-350 parts of water. A four-component repair system composed of the microbial self-repairing agent, the oxygen slow-release agent, the probiotics-loaded expanded perlite and the nutrient-loaded expanded perlite is combined with the polypropylene fiber to form the crack depth-width three-dimensional self-repairing concrete. The concrete can remedy the deficiency that the crack depth-direction repaireffect of a current concrete crack self-repairing technology is poor, the durability of the concrete is improved, and meanwhile the concrete is environmentally friendly and light and has a heat insulation function.