The invention provides a definition method of the window period of decay of cyanophyta. The definition method comprises the steps that samples are collected from the lake site every month throughout the year, RNA extraction and purification is performed on cyanophyta samples from field lake water samples and indoor pure culture cyanophyta samples in the logarithmic growth period, the relative expression of a nblA gene is measured, the ratio of dissolved glucose/neutral polysaccharide in the field lake water samples is determined, and the period of decay of the cyanophyta is synthetically identified. The definition method is high in sensitivity, fast and accurate, and is not affected by the disturbance of water particles.