The compositional tunability of non-isovalent multicomponent chalcogenide thin films and the extent of atomic ordering of their crystal structure is key to the performance of many modern technologies. In contrast, the effects of ordering are rarely studied for quantum-confined materials, such as colloidal nanocrystals. In this paper, the possibilities around composition tunability and atomic ordering are explored in ultrasmall ternary and quaternary quantum dots, taking I-III-VI-group Cu-Zn-In-Se semiconductor as a case study. A quantitative synthesis for 3.3 nm quaternary chalcogenide nanocrystals is developed and shown that cation and cationic vacancy ordering can be achieved in these systems consisting of only 100s of atoms. Combining experiment and theoretical calculations, the relationship between structural ordering and optical properties of the materials are demonstrated. It is found that the arrangement and ordering of cationic sublattice plays an important role in the luminescent efficiency. Specifically, the concentration of Cu-vacancy couples in the nanocrystal correlates with luminescence quantum yield, while structure ordering increases the occurrence of such optically active Cu-vacancy units. On the flip side, the detrimental impact of cationic site disorder in I-III-VI nanocrystals can be mitigated by introducing a cation of intermediate valence, such as Zn (II).