To explore the influencing factors of the pulsed electric field on the prevention and control of aquatic organism fouling, and to determine the minimum electric field conditions required for effective prevention and control of fouling organisms, we built a pulsed electric field test platform. Approximate square wave pulses were generated by the pulse forming network. During the experiment, we recorded the death rate and morphological structure changes of the Daphnia magna. With the help of Matlab nonlinear fitting, we obtained the functional relationship between the pulsed electric field-induced death rate and the electric field strength, the total equivalent processing time, and the pulse injection energy density. The paper takes a main canal project as an example to introduce the principle of parameter selection and platform construction method of pulsed electric field for controlling large water fleas. The results showed that the treatment effect of the pulsed electric field on the Daphnia magna is positively correlated with the electric field strength, the total equivalent treatment time and the pulse injection energy density. When the electric field strength is between 0.5 and 1.5 kV/cm, the induced mortality increases by about 35% for every 0.5 kV/cm increase in the electric field strength. When the electric field strength is higher than 2.0 kV/cm, the total equivalent processing time is higher than 900 μs, or the pulse injection energy density is higher than 80 J/L, the pulsed electric field can produce more than 80% induced mortality.