The geometry in self-assembled superlattices of colloidal quantum dots (QDs) strongly affects their optoelectronic properties and is thus of critical importance for applications in optoelectronic devices. Here, we achieve the selective control of the geometry of colloidal quasi-spherical PbS QDs in highly-ordered two and three dimensional superlattices: Disordered, simple cubic (sc), and face-centered cubic (fcc). Gel permeation chromatography (GPC), not based on size-exclusion effects, is developed to quantitatively and continuously control the ligand coverage of PbS QDs. The obtained QDs can retain their high stability and photoluminescence on account of the chemically soft removal of the ligands by GPC. With increasing ligand coverage, the geometry of the self-assembled superlattices by solution-casting of the GPC-processed PbS QDs changed from disordered, sc to fcc because of the finely controlled ligand coverage and anisotropy on QD surfaces. Importantly, the highly-ordered sc supercrystal usually displays unique superfluorescence and is expected to show high charge transporting properties, but it has not yet been achieved for colloidal quasi-spherical QDs. It is firstly accessible by fine-tuning the QD ligand density using the GPC method here. This selective formation of different geometric superlattices based on GPC promises applications of such colloidal quasi-spherical QDs in high-performance optoelectronic devices.