In order to reduce the underwater electric field generated by corrosion of ship, a boundary element method (BEM) combined with nonlinear polarization curve was employed to investigate the influence of output current of compensate anode in an electric field protection system on underwater electric field. Moreover, the BEM model was verified by physical scale modeling (PSM). The distribution characteristic of electric field and the variation trend of electric field with compensate current obtained by simulation are consistent with the experimental results. Moreover, the errors of peak-to-peak value of electric field obtained by experiment and simulation are within 20%. Compared with 0 mA compensation current, the peak-to-peak values of X component, Y component, Z component, and modulus are reduced by 52%, 70%, 72%, and 62% respectively when compensation current is 40 mA. The phenomenon of over-compensation will occur if compensation current is greater than 40 mA.