The invention provides a method and system for deeply treating coking wastewater to decarbonize, decolor and remove cyanide. The method comprises the following steps: 1) introducing the coking wastewater into a Fenton fluidized bed, and adding a mixed solution of ferrous sulfate, sulfuric acid and water into a solution; 2) adding hydrogen peroxide into the solution of the Fenton fluidized bed and sufficiently reacting; 3) leading out a reaction solution in the Fenton fluidized bed, adjusting the pH (Potential of Hydrogen) value of the reaction solution, adding a flocculating agent, and after precipitating, taking supernatant; 4) mixing the supernatant with sodium hypochlorite, and carrying out an oxidization reaction; and 5) adjusting the pH of the reaction solution, and carrying out adsorption treatment by active carbon to obtain a deeply treated water body. According to the method and the system, the Fenton fluidized bed, flocculation and sedimentation, sodium hypochlorite oxidization, and active carbon filtering and adsorption are effectively combined; the Fenton fluidized bed and the flocculation and sedimentation are carried out, residual cyanide in output water mainly exists in a CN<-> form, the oxidization efficiency of the sodium hypochlorite is higher, and the cyanide can be removed; and the adsorption effect of the active carbon is combined, so that the water concentration of the output water is lower.