Ultrasound atomic force microscopy (US-AFM) has been used for subsurface imaging of nanostructures. The contact stiffness variations have been suggested as the origin of the image contrast. Therefore, to analyze the image contrast, the local changes in the contact stiffness due to the presence of subsurface features should be calculated. So far, only static simulations have been conducted to analyze the local changes in the contact stiffness and, consequently, the contrast in US-AFM. Such a static approach does not fully represent the real US-AFM experiment, where an ultrasound wave is launched either into the sample or at the tip, which modulates the contact stiffness. This is a time­dependent nonlinear dynamic problem rather than a static and stationary one. This paper presents dynamic 3D ultrasound analysis of contact stiffness in US-AFM (in contrast to static analysis) to realistically predict the changes in contact stiffness and thus the changes in the subsurface image contrast. The modulation frequency also influences the contact stiffness variations and, thus, the image contrast. The three-dimensional time-dependent ultrasound analysis will greatly aid in the contrast optimization of subsurface nano imaging with US-AFM.