The submerged body near the free surface is disturbed by the 1st and 2nd order wave forces, which results in unstable movements when no control is applied. In this paper, the vertical motions of the submerged body are analyzed, and the time-variant nonlinear system for the vertical motions of the submerged body is transformed to the time-invariant linear system in state space. Next, depth controller of the submerged body is designed by using LQR control, one of the modern optimal control technique. Numerical simulation shows that effective depth controls can be achieved by LQR control.