ISWS (internal solitary waves) frequently occur in stratified oceans, leading to flow fields that produce opposing flow directions and intense shear between the upper and lower layers of the pycnocline. This research explores the essential dynamics between submerged bodies and oceanic internal waves. The study presents a numerical flume for internal solitary waves, constructed based on the mKdV (modified Korteweg-de Vries) theory. Besides, it proposes a control approach for a submerged body encountering internal solitary waves in layered fluids. The results indicate that the control strategy effectively suppresses the heaving and pitching motions of the submerged body, with the most significant improvement observed in the pitch angle. Under the S control strategy, the magnitude of pitch angle can be kept within a fluctuation range of 0.05 rad. In addition, the trajectory of the uncontrolled submerged body is similar to a tangent curve, while the submerged body with control measures sinks/rises with the wave surface in a “U” shape.