In metal nanoparticles (NPs) supracrystals, the metallic core provides some key properties, e.g. magnetization, plasmonic response or conductivity, with the ligand molecules giving rise to others like solubility, assembly or interaction with biomolecules. The formation of these supracrystals depends on a complex interplay between many forces, some stemming from the core, some from the ligands. At present, there is no known approach to characterize the local order of ligand molecules or their dynamics with atomic spatial resolution. Here, we develop a methodology based on small-angle ultrafast electron diffraction combined with angular cross-correlation analysis to characterize a two-dimensional supracrystal of dodecanethiol-coated gold NPs. We retrieve the static arrangement of the ligands, showing that at equilibrium they order in a preferential orientation on the NPs surface and throughout the two-dimensional supracrystal. Upon light excitation, positional disorder is induced in the supracrystal, while its overall homogeneity is surprisingly found to transiently increase. This suggests that transient annealing of the supracrystal takes place within few picoseconds (ps). This methodology will enable the systematic investigation of the dynamical structural properties of nano-assembled materials containing light elements, relevant for biological applications.