The invention discloses a controlled release fertilizer with high content of biological carbon and a preparation method thereof. The controlled release fertilizer mainly comprises a controlled release agent with high content of biological carbon and a fertilizer, wherein the controlled release agent with high content of biological carbon comprises a polymer, biological carbon, an adsorbent and a catalyst, wherein the weight ratio of the polymer is 0.1-50%, the weight ratio of the biological carbon is 50-90%, the weight ratio of the adsorbent is 1-10%, and the particle size of the controlled release agent is 60-200 meshes. In the method of the invention, by applying the controlled release agent to the formula and the manufacturing process of fertilizer production and further combining the biological carbon with a polymerization micromatrix, the controlled release fertilizer prepared by the polymerization micromatrix with high content of biological carbon has various controlled release mechanisms of nutrient components required for plant growth and can increase the carbon cycle of biological substances, improve the soil and reduce the greenhouse gases in farmlands such as emission of CH4,N2O and the like, thus the controlled release fertilizer is a high-efficiency fertilizer capable of storing carbon in the soil, reducing emission and controlling release.