The invention discloses a method for preventing silt and reducing silt of an excavated harbour basin. According to the method, a pump room, water pumps, water diversion culvert pipes and water outletheads are arranged; the two ends of each water diversion culvert pipe are respectively connected with a water taking head and a water outlet head, and each water diversion culvert pipe is connected with a corresponding water pump, so that the water pump dries water to circulate to pump water on along a water surface upstream the harbour basin and spray water back to the water surface in the harbour basin. Harbour basin silt deposition calculation is performed by two steps by establishing a mathematical model: step one, establishing a plane two-dimensional water-sediment transportation mathematical model; and step two, performing silt back calculation of the excavated harbour basin, designing two water sucking and spraying schemes for preventing the silt and reducing the silt of the excavated harbour basin in a flood period and a measure of inhibiting backflow to reduce silt deposition and calculating harbour basin silt deposition. According to the method, the purposes of preventing thesilt and reducing the silt are achieved by controlling a boundary layer to separate and damage the backflow; the method is scientific in design, and a silt reducing effect is obvious; the problem about water environment in the harbour basin is also solved; oil contamination water pollution, agricultural waste water pollution and thermal pollution in the harbour basin are reduced; a harbour is protected; and the water body quality is improved.