The invention discloses an environmentally friendly biochar-based fertilizer and an application method thereof. The preparation of the biochar-based fertilizer comprises the following steps of: drying and crushing forestry and agricultural residues, then performing oxygen limited pyrolysis on the crushed materials for 1-5 hours at 300 to 700 DEG C, and sieving, thereby obtaining biochar; and after the biochar is fixed with persistent organic pollutant degrading bacteria, mixing the biochar with a fertilizer, stirring the two thoroughly, and adding a binder accounting for 1wt%-4wt% of the total weight, thus obtaining the environmentally friendly biochar-based fertilizer. For application, the prepared environmentally friendly biochar-based fertilizer is applied to soil by 100-1000 kg per hectare; the surface layer of soil, to which the biochar-based fertilizer is applied previously, is turned over by 0-20 cm, so that the biochar-based fertilizer is mixed with the soil thoroughly, and then the soil can be used for planting crops. The environmentally friendly biochar-based fertilizer provided by the invention overcomes the shortcoming that present biochar-based fertilizers contain organic pollutants such as polycyclic aromatic hydrocarbon, the influence of the fertilizer on soil and environment is alleviated, and the safety risk of agricultural products is reduced; moreover, the environmentally friendly biochar-based fertilizer has the advantages of simple and practicable preparation process, low cost and the like.