Perovskite nanocrystal superlattices are being actively studied after reports have emerged on collective excitonic properties at cryogenic temperatures, where energetic disorder is minimized due to the frozen lattice vibrations. However, an important issue related to structural disorder of superlattices at low temperatures has received little attention to date. In this work, it is shown that CsPbBr3 nanocrystal superlattices undergo a reversible order–disorder transition upon cooling to 90 K. The transition consists of the loss of structural coherence, that is, increased nanocrystal misalignment, and contraction of the superlattices, as revealed by temperature‐dependent X‐ray diffraction, and is ascribed to the solidification of ligands (on the basis of Raman spectroscopy). Introducing shorter amines on the nanocrystal surface allows to mitigate these changes, improve order, and shorten interparticle distance. It is demonstrated that the low temperature phase of the short ligand‐capped nanocrystal superlattices is characterized by a strong exciton migration observable in the photoluminescence decay, which is due to the shrinkage of the inter‐nanocrystal distance.