The invention provides a method of extracting a weak target signal in ocean current interference. The method comprises the following steps: ocean magnetic field variation information f0i is acquired; multi-scale decomposition is carried out on the f0i to obtain a signal f1i; a stochastic resonance method is adopted for the f1i; a fourth-order Runge-Kutta method is used for high-accuracy numerical value solution on a nonlinear stochastic resonance system; optimal stochastic resonance parameters are found out; the best resonance output data sequence f2i is solved; multi-scale decomposition is carried out on the f2i; different thresholds are selected in a main frequency band interval where the target signal is to rebuild a signal f3i through threshold processing; feature extraction is carried out on the f3i; and extracted feature parameters are matched and compared with a database for underground target motion. Abnormal target disturbance magnetic field features are screened from complex ocean background electromagnetic interference, a passing underwater moving target can be indirectly detected, discovered and recognized, and the underwater prediction and early warning ability can be effectively improved.