Nanoindentaiton testing has revealed pop-in events in load–displacement curves of relaxor single crystal PMN-0.3PT ferroelectric materials that occur when the indentation depth is small (e.g., dozens of nanometers). Although there has been speculation of an occurrence of phase transition, there is a relative lack of investigation on the domain evolution associated with the phase transition when the pop-in events appear. In the present study, nanoindentation of this material was systematically modeled using phase-field simulations, which capture the domain and phase evolution of a PMN-0.3PT ferroelectric single crystal. The results, qualitatively similar to the experimental results, revealed details of the contribution of phase transformations to pop-in events. The influence of indenter shape, size, and external electric field on the pop-in event was also examined. This work provides a computational evaluation of the effects of the phase transition mechanism in ferroelectric materials under nanoindentation and gives insight into local mechanical loading effects on these electromechanically coupled crystals.