In this paper a method is presented to estimate the unknown parameters of nonlinear El Nio/La Nio-Southern Oscillation model based on the variational principle. Firstly, the equation of the coupled air-sea model is included into the objective functional. Secondly, the formulas of the adjoint equation and the functional gradient for unknown parameters are derived using the variational method. Finally, the algorithm to estimate unknown parameters of air-sea oscillator system is designed according to the above formulas. The numerical simulation results show that the proposed method is very effective and feasible to estimate the unknown parameters of nonlinear air-sea coupled dynamical system.