A new procedure for designing optimal bounded control of quasi-nonintegrable Hamiltonian systems with actuator saturation is proposed based on the stochastic averaging method for quasi-nonintegrable Hamiltonian systems and the stochastic maximum principle. First, the stochastic averaging method for controlled quasi-nonintegrable Hamiltonian systems is introduced. The original control problem is converted into one for a partially averaged equation of system energy together with a partially averaged performance index. Then, the adjoint equation and the maximum condition of the partially averaged control problem are derived based on the stochastic maximum principle. The bounded optimal control forces are obtained from the maximum condition and solving the forward–backward stochastic differential equations (FBSDE). For infinite time-interval ergodic control, the adjoint variable is stationary process, and the FBSDE is reduced to an ordinary differential equation. Finally, the stationary probability density of the Hamiltonian and other response statistics of optimally controlled system are obtained by solving the Fokker–Plank–Kolmogorov equation associated with the fully averaged Itô equation of the controlled system. For comparison, the bang–bang control is also presented. An example of two degree-of-freedom quasi-nonintegrable Hamiltonian system is worked out to illustrate the proposed procedure and its effectiveness. Numerical results show that the proposed control strategy has higher control efficiency and less discontinuous control force than the corresponding bang–bang control at the price of slightly less control effectiveness.