The invention discloses a directive breeding method for culturing pond diatom in fresh water. By regulating the contents of nitrogen, phosphorus, silicates and minor elements in the culture pond and considering the pH value and diatom inoculation concentration, favorable algal facies using diatom as the dominant species are directively bred in the pond, thereby promoting the mass reproduction of the pond diatom, preventing the outbreak of the high-yield culture pond blue algae, and increasing the culture yield. Besides, the method can effectively regulate the water quality, reduce the disease incidence rate and enhance the culture yield and culture product quality. The method is simple, does not need any supporting facility, and can be popularized and applied more easily.