The invention discloses a method for removing algae and microcystin from raw water in a water plant. The method comprises the following steps of: A, biofilm culturing of fillers: placing selected carrier fillers in a water source site, culturing and transferring to a biofilm reactor; B, treatment through the biofilm reactor: removing algae in water by utilizing the interception effect of a biofilm in the biofilm reactor to algae cells and the ingestion effect of microfauna in the biofilm; C, regulation and control and treatment through oleic acid: regulating and controlling the removal effectof the biofilm reactor to the microcystin by using the oleic acid so as to improve the removal rate of the biofilm reactor to the algae cells; D, treatment through a sedimentation tank; and E, treatment through activated carbon: treating effluent water of the biofilm reactor through the sedimentation tank and thoroughly removing incompletely-degraded microcystin by utilizing the strong adsorptioneffect of the activated carbon so that the effluent water reaches the sanitary standard for drinking water in China. The method for removing algae and microcystin from the raw water in the water plant can be used for effectively removing the microcystin and is highly-efficient, economic, simple and feasible; and by means of the method, the removal rate of the algae cells reaches 90-95 percent, and the microcystin removal ratio reaches 95-100 percent.