The viability of neural probes with microelectrodes for neural recording and stimulation in the brain is important for the development of neuroprosthetic devices. Vertically aligned nanowire microelectrode arrays can significantly enhance the capabilities of neuroprosthetic devices. However, when they are implanted into the brain, micromotion and mechanical stress around the neural probe may cause tissue damage and reactive immune response, which may degrade recording signals from neurons. In this research, a finite-element model of the nanowire microelectrode and brain tissue was developed. A rigid body method was provided, and the simulation efficiency was significantly increased. The interface between the microelectrode and brain tissue was modeled by contact elements. Brain micromotion was mimicked by applying a displacement load to the electrode and fixing the boundaries of the brain region. It was observed that the vertically aligned nanostructures on the electrode of the neural probe do increase the cellular sheath area. The strain field distributions under various physical coupling cases at the interface were analyzed along with different loading effects on the neural electrode.