Dynamical structural defects exist naturally in a wide variety of solids. They fluctuate temporally and hence can deteriorate the performance of many electronic devices. Thus far, the entities of these dynamic objects have been identified to be individual atoms. On the other hand, it is a long-standing question whether a nanocrystalline grain constituted of a large number of atoms can switch, as a whole, reversibly like a dynamical atomic defect (that is, a two-level system). This is an emergent issue considering the current development of nanodevices with ultralow electrical noise, qubits with long quantum coherence time, and nanoelectromechanical system sensors with ultrahigh resolution. We demonstrate experimental observations of dynamic nanocrystalline grains that repeatedly switch between two or more metastable coordinate states. We study temporal resistance fluctuations in thin ruthenium dioxide (RuO2) metal nanowires and extract microscopic parameters, including relaxation time scales, mobile grain sizes, and the bonding strengths of nanograin boundaries. These material parameters are not obtainable by other experimental approaches. When combined with previous in situ high-resolution transmission electron microscopy, our electrical method can be used to infer rich information about the structural dynamics of a wide variety of nanodevices and new two-dimensional materials.