A method was developed to control heterotrophic bacteria in cooling water by mixing non-oxidizing (Isothiazolinones)and oxidizing sterilization (Hydantoin)together. The result of disinfection test shows that the agent possesses a higher efficiency. At the same time the method introduced polyepoxysuccinic acid—1-Acrylanmido-2-methylpropanesul fonic acid(PESA-AMPS (10%)) in to the disinfection system. The rotary coupon test and aeration scale inhibition method show that the bactericidal agent also possesses higher anti-corrosion and inhibition rate. The concentration of heterotrophic bacteria can well be controlled below 105cfu/mL when the additional quantity of the agent changes from 100mg/L to 200mg/L.