Colloidal PbS quantum dots (QDs) are attractive for solution-processed thin-film optoelectronic applications. In particular, directly achieving QD thin-films by printing is a very promising method for low-cost and large-scale fabrication. The kinetics of QD particles during the deposition process play an important role in the QD film quality and their respective optoelectronic performance. In this work, the particle self-organization behavior of small-sized QDs with an average diameter of 2.88 ± 0.36 nm is investigated for the first time in situ during printing by grazing-incidence small-angle X-ray scattering (GISAXS). The time-dependent changes in peak intensities suggest that the structure formation and phase transition of QD films happen within 30 seconds. The stacking of QDs is initialized by a templating effect, and a face-centered cubic (FCC) film forms in which a superlattice distortion is also found. A body-centered cubic nested FCC stacking is the final QD assembly layout. The small size of the inorganic QDs and the ligand collapse during the solvent evaporation can well explain this stacking behavior. These results provide important fundamental understanding of structure formation of small-sized QD based films prepared via large-scale deposition with printing with a slot die coater.