In this paper a method is proposed to estimate the unknown parameters of nonlinear map based on the second-order discrete variational method. On the basis of adjoint equations and gradient expressions of cost functional derived from variational method, the second-order adjoint equations and the exact formulas for the Hessian-vector product are educed using the second-order discrete variational method. A new algorithm is given for estimating the unknown parameters of nonlinear maps. The numerical simulations show that all unknown physical parameters of Hyperhenón map and two-dimensional parabolic map are estimated successfully and precisely. Simulation results also demonstrate the validity and advantages of second-order discrete variational method of estimating the parameters of the discrete chaotic systems.