The invention discloses an environment-friendly flocculating agent for lowering the COD and a preparation method and application thereof. The environment-friendly flocculating agent is prepared from, by mass, 1%-5% of cationic starch, 1%-3% of chitosan, 1%-3% of sepiolite, 1%-5% of sodium chloride, 0.2%-1% of rectorite, 1%-3% of glacial acetic acid and 80%-94.8% of water. The preparation method comprises the steps that the water is added into a reactor, heated and stirred; the cationic starch is added into the reactor, the glacial acetic acid and the chitosan are added when the starch is completely dissolved, the sodium chloride, the sepiolite and the rectorite are added when the chitosan is completely dissolved, fully stirring is performed, when the materials are completely dissolved, the mixed liquid is cooled to the room temperature, and then the environment-friendly flocculating agent is prepared. The environment-friendly flocculating agent is natural, degradable and friendly to environment and cannot cause secondary pollution; paint slag agglomeration can be improved, the paint slag water content can be increased, and the COD removing rate of painting workshop circulating water is about 90 percent.