The invention discloses modified polyurethane suspended filler which comprises, by weight, 10 parts to 80 parts of polyhydroxyalkanoate, 10 parts to 80 parts of activated carbon, 60 parts to 80 parts of polyurethane, 1 part to 10 parts of water-soluble polyurethane solutions, 0 part to 10 parts of bioactivator, 0 part to 1 part of inorganic metal salt, 0 part to 20 parts of organic high-molecular polymer and 0 part to 10 parts of inorganic flocculate. A preparation method of the modified polyurethane suspended filler includes the steps of taking the 10 parts to 80 parts of polyhydroxyalkanoate, the 10 parts to 80 parts of activated carbon, the 0 part to 10 parts of bioactivator, the 0 part to 1 part of inorganic metal salt, the 0 part to 20 parts of organic high-molecular polymer and the 0 part to 10 parts of inorganic flocculate, dissolving the mixture in the 1 part to 10 parts of water-soluble polyurethane solutions, soaking the 60 parts to 80 parts of polyurethane in the solution to obtain the loaded polyurethane suspended filler, and conducting secondary drying after primary drying is conducted to obtain the modified polyurethane suspended filler. The modified polyurethane suspended filler has the advantages of being high in porosity and large in specific area.