We have developed several methods for the optimization problem having large-scale and highly nonlinear system. First, step by step method in optimization process was employed to improve the convergence. In addition, techniques of furnishing good initial guesses for analysis using sensitivity information acquired from optimization iteration, and of manipulating analysis/optimization convergency criterion motivated from simultaneous technique were used. We applied them to flow control problem and verified their efficiency and robustness. However, they are based on quasi-Newton method that approximate the Hessian matrix using exact first derivatives. However solution of the Navier-Stokes equations are very cost, so we want to improve the efficiency of the optimization algorithm as much as possible. Thus we develop a true Newton method that uses exact Hessian matrix. And we apply that to the three-dimensional problem of flow around a sphere. This problem is certainly intractable with existing methods for optimal flow control. However, we can attack such problems with the methods that we developed previously and true Newton method.