The structure of 3 nm ZnS nanoparticles differs from that of bulk ZnS and is shown to vary with the particle aggregation state. Dispersed or weakly aggregated nanoparticles in suspension have a more distorted internal structure than strongly aggregated nanoparticles. Reversible switching between distorted and crystalline structures can be induced by changing the aggregation state via slow drying and ultrasonic agitation. The transformation was analyzed using pair distribution function data from wide angle x-ray diffraction and the aggregation state monitored via small angle x-ray scattering. Molecular modeling provides insight into particle-particle interactions that induce the structural changes. The reversible nature also implies a low activation energy of nanoparticle transformation and indicates that distorted nanoparticles are not trapped in a metastable state.