The invention provides a process for eliminating algae in cooling water system comprising the steps of, filling bactericide and basic substance into cooling water, making the pH value to be 9-14, mixing one or more from Li2O, Na2O, K2O, LiOH, NaOH, KOH, Li2Co3, Na2Co3, K2Co3, LiHCo3, NaiHCo3, KHCo3, Na3PO4, K3PO4, sodium acetate and postassium acetate. While the bactericidal agent is a mixture two or more selected from chlorine, sodium hypochlorite, potassium hypochlorite, calcium hypochlorite, dichloroisocyanuric acid, trichloroiminocyanuric acid, chlorine dioxide, bromine, sodium hypochlorite, potassium hypochlorite, calcium hypochlorite, hydrogen dioxide solution, ozone, quaternaries, and glutaric dialdehyde.