The invention discloses a method for storing a micro-algae bait. The method comprises the following steps: uniformly mixing a PH buffering solution, a cell protective agent and concentrated organic acids, preservatives and antibiotic solutions with the high-cell-concentration micro-algae bait which is obtained by performing fermentation according to certain volume ratios to obtain a mixture; subsequently, putting the mixture under a light-proof condition that a temperature is 0 DEG C to 10 DEG C and storing the mixture. In the method, the added materials cannot produce toxic and harmful effects on micro-algae cells, on the contrary, an acid-alkali system of the micro-algae bait also can be maintained, so that pollution of mixed bacterium during preservation is avoided, the biological activity of the micro-algae bait is maintained to the maximum extent, the consumption of the antibiotics and the preservatives brought into a water body is relatively low, and pollution to the water body is avoided.