We have prepared thin films of PbSe quantum dots (QDs) featuring three different ligands, oleic acid (OA), butylamine (BA), and 1,2-ethanedithiol (EDT), which have pronounced affects on the arrangement and photovoltaic performance of the PbSe QDs in the thin films. Transmission electron microscopy revealed that ligands that altered the inter-QD spacing induced significant changes in the packing of the PbSe QDs in localized regions of small areas (300 × 300 nm) of the thin films: from a superlattice of OA-capped PbSe QDs to a chaotic pattern of EDT-capped PbSe QDs. Using a synchrotron X-ray reflectivity probe and data fitting, we determined that the roughness decreased and the average densities increased for large-area (1.5 × 1.5 cm) PbSe QD thin films capped with BA and EDT, relative to those of the OA-capped PbSe QD film. In particular, the PbSe QDs' vertical packing density, which is critical for charge transport, increased substantially for the system incorporating EDT ligands. As a result, devices containing the EDT-treated PbSe QD film as the active layer displayed much improved power conversion efficiencies (PCEs) relative to those of corresponding devices featuring either the OA- or BA-capped PbSe QD films as active layers. Adopting a layer-by-layer technique, we fabricated a EDT-capped PbSe QD device that exhibited a PCE of 2.45%.