The ligand exchange process is a key step in fabrications of quantum dot (QD) optoelectronic devices. In this work, on the basis of grazing incidence X-ray scattering techniques, we find that the ligand exchange process with halide ions changes the PbS QD superlattice from face-centered-cubic to body-centered-cubic stacking, while the QD crystal lattice orientation also changes from preferentially “edge-up” to “corner-up”. Thus, the QDs’ shape is supposed to be the main factor for the alignment of QDs in close packed solids. Moreover, we tailor the alignment of the close packed solids by thermal treatments and further investigate their inner charge carrier dynamics by pump–probe transient absorption experiments. An overall better structure alignment optimizes the charge carrier hopping rate, as confirmed by the time dependence of the photon bleaching peak shift. The QD solid treated at 100 °C shows the best inner structure alignment with the best charge carrier hopping rate.