The invention discloses a biological soil restoration fertilizer. The fertilizer is prepared from, by weight, 32-36 parts of biogas slurry, 4-5 parts of saccharomyces cerevisiae, 6-9 parts o brown sugar, 3-4 parts of calcium powder, 1-2 parts of copper sulphate pentahydrate, 26-30 parts of flax fiber bundles, 15-17 parts of siderite slag, 15-17 parts of limonite slag, 68-70 parts of orange peels, 3-6 parts of an EM compound microbial agent and a defined amount of water. By means of the biological soil restoration fertilizer, biological activity of soil can be effectively improved, growth and expanding of plant roots are facilitated, water permeability and air permeability of the soil are improved, the soil is prevented from being eroded by bacteria and pests, healthy growth of plants is promoted, meanwhile, heavy metal can be subjected to a precipitation reaction, a chelation reaction and other reactions in the soil, bio-availability of the heavy metal is lowered, the absorbing capacity of the crops for the heavy metal is reduced, quality of agricultural products is improved, and the ecological environment of the soil is restored.