The invention belongs to the fields of chemical industry and water treatment, and in particular relates to a compound bacteria and algae inhibitor and its application. The composite bacteria and algae inhibitor of the present invention contains isothiazolinone, 2,2-dibromo-3-nitrilopropionamide, solvent and water, and the mass percentages of each component are respectively 1% to 40% of isothiazolinone, 2,2-dibromo-3-nitrilopropionamide 5%-40%, solvent 20%-60%, water 10-70%. The compound bacteria and algae inhibitor of the present invention is a non-oxidative biocide. When the bacteria and algae inhibitor is applied to a water treatment system, the impact type intermittent dosing method is adopted, and the dosage of the bacteria and algae inhibitor per liter of water is 1 mg to 100 mg. . The components of the formula of the present invention have obvious synergistic effect, good compatibility with scale inhibitors and corrosion inhibitors, low biological toxicity, high biodegradable rate, and have killing and inhibiting effects on planktonic bacteria and algae in water, It has stripping and inhibiting effects on the bacteria and algae adherents that grow on the surface of the equipment. In practical application, it has the advantages of small addition amount, low use cost, convenient operation and no pollution.