The invention discloses a preparation method of a biological carbon fertilizer. The preparation method comprises the following steps of 1, using biological carbon, nitric acid and ammonia water to prepare a reaction product A; 2, fully stirring and uniformly mixing the reaction product A, a phosphate fertilizer, azotobacter, plant vinegar liquid, waste molasses and a fertilizer additive; 3, granulating; 4, uniformly mixing humic acid powder, bentonite, calcium oxide and diatomite, so as to obtain a material B; 5, coating by a slow-release coating material, so as to obtain a particle B; 6, using the material B to perform fertilizer coating on the particle B, so as to obtain a particle C; 7, further drying the prepared particle C. The preparation method has the beneficial effects that before crop is planted, the fertilizer is applied onto the soil surface, the fertilizer with ploughing type fertilizer surface layer acts onto the soil, the surface fertilizer contains the humic acid, and the inner layer is a coated biological carbon-based slow-release fertilizer; the fertilizer is reasonably applied, the fertility of the soil is improved, and the heavy metal and other pollutants are effectively prevented from entering the food chain.