A new procedure for designing optimal control of quasi non-integrable Hamiltonian systems under stochastic excitations is proposed based on the stochastic averaging method for quasi non-integrable Hamiltonian systems and the stochastic maximum principle. First, the control problem consisting of 2 n -dimensional equations governing the controlled quasi non-integrable system and performance index is converted into a partially averaged one consisting of one-dimensional equation of the controlled system and performance index by using the stochastic averaging method. Then, the adjoint equation and the maximum condition of the partially averaged control problem are derived based on the stochastic maximum principle. The optimal control forces are determined from the maximum condition and solving the forward–backward stochastic differential equations (FBSDE). For infinite time-interval ergodic control, the adjoint variable is a stationary process and the FBSDE is reduced to a partial differential equation. Finally, the response statistics of optimally controlled system is predicted by solving the Fokker–Plank equation (FPE) associated with the fully averaged Itô equation of the controlled system. An example of two degree-of-freedom (DOF) quasi non-integrable Hamiltonian system is worked out to illustrate the proposed procedure and its effectiveness.