The invention discloses a biological sediment modifier for a fishpond, belonging to the technical field of water quality purification of fishponds. The biological sediment modifier is prepared from the following raw materials in parts by weight: 3-8 parts of bacillus subtilis powder, 3-8 parts of nitrifying bacteria powder, 3-8 parts of denitrifying bacteria powder, 3-8 parts of sulfurizing bacteria powder, 10-40 parts of zeolite powder, 40-70 parts of sodium humate, and 0.5-3 parts of calcium peroxide, wherein the total content of viable bacteria is 2*10<8>-2*10<9> per gram. The biological sediment modifier disclosed by the invention can be used for absorbing the nutrition of sediment, and forming a bacterium membrane on the sediment via fermentation, breeding and bacterial community expansion, so as to cover the sediment and prevent the sediment from polluting water quality, thus benefiting the growth of aquatic animals, greatly increasing a degradation rate, and avoiding the secondary pollution of chemical degradation to a water body.