The invention discloses a method for preparing a microbial flocculant through enteromorpha hydrolysate fermentation. The method comprises the steps of preparation of liquid strain, fermentation and product aftertreatment. The fermentation process comprises the steps that 1, fresh enteromorpha is cleaned, salt, sediment and unwanted algae are removed, then the fresh enteromorpha is smashed and added to a hydrolysis tank, water is added to regulate acidity, alkali is added for neutralization, filter pressing and clarification are conducted, and then a hydrolysate is obtained; 2, the hydrolysate is diluted till the sugar concentration of reducing sugar is 15-30 g / L, fermentation liquor is prepared and added to a fermentation tank, and high-temperature sterilization and cooling are conducted; 3, a seed solution is inoculated into the fermentation tank for fermentation, and fermentation is ended after the content of residual sugar in the fermentation liquor is reduced to the level below 3 g / L. According to the method, enteromorpha is used as the raw material, microbial flocculant fermentation is directly conducted after acid hydrolysis filtration, the production method is simple, production cost is low, grain is saved, and waste is turned into wealth.