The pulsed discharge process in water is complex and there is no clear functional relationship between the discharge parameters and the discharge deposition energy. To obtain the optimum deposition energy, clarify the influence of different discharge parameters on the deposition energy and obtain the best combination of discharge parameters, this paper builds a high-voltage pulse discharge test platform in water and investigates the influence of three discharge parameters, namely voltage, electrode spacing and conductivity, on the deposition energy of discharge in water by combining with the Kriging agent model. The optimal combination of discharge parameters was determined by using a genetic algorithm. The results of the study show that: the root mean square error of the model is 6.95%, which satisfies the accuracy requirement through cross-validation; the deposition energy varies with multiple peaks under the synergistic effect of electrode spacing and conductivity at a certain applied voltage; the best combination of voltage, electrode spacing and conductivity is 17 kV, 2.28 mm and 0.8 mS/cm respectively, which produces the highest deposition energy. The relative deviation between predicted and actual values at the optimum point were experimentally verified to be within 8%.