Quantum dots (QDs) have attracted much attention due to their unique physicochemical properties depending on the size and shape of particles. Enhancing the performance of these QDs requires achieving a uniform morphology and narrowing their size distribution. Recently, we successfully developed plasmonic thin-layer chromatography (TLC) as a technique for nanoparticle (NP) separation, in which QDs were optically captured through the photoexcitation of Au NPs immobilized on TLC plates. Here, we report the size separation of rod-shaped Zn−Ag−In−S (ZAIS) QDs with different lengths (16−31 nm) but with a constant width (ca. 4 nm). An irradiation of 820 nm monochromatic light photoexcited a localized surface plasmon resonance peak of Au NPs immobilized on TLC plates, resulting in optical trapping of rod-shaped ZAIS QDs within the Au NP-immobilized region, in which the minimum length of trapped QDs became shorter with an increase in irradiation intensity. Based on this behavior, we separated polydisperse rod QDs into two groups of QDs having different lengths with a relatively narrow distribution. Ellipsoidal ZAIS QDs with lengths of 8−19 nm were also prepared. The energy gap of those QDs was constant at 1.9 eV, regardless of the QD length, being much smaller than the energy gaps of rod-shaped ZAIS QDs, 2.6−3.1 eV. When comparing the two types of QDs with different shapes but similar lengths, we observed that the threshold irradiation intensity required for QD trapping was lower for ellipsoidal particles than that for rodshaped ones. To explain this behavior, we conducted theoretical simulations, which revealed that the optical forces (attractive forces) between ZAIS QDs and Au NPs were modulated by variations in the polarizability of QDs. The variations originated from changes in both particle volume and optical properties. These results provided valuable knowledge about the influence of size, shape, and optical properties on the QD separation process with plasmonic TLC.