Theoretical understanding of the surface modification of Cl-passivated silicon nanocrystals (Si NCs) is rather limited, in stark contrast to that for H-passivated Si NCs. We now investigate four surface-modification schemes (silanization, alkylation, alkoxylation and aminization) that have been experimentally adopted for Cl-passivated Si NCs in the framework of density functional theory. It is found that aminization most significantly affects the electronic structures of Si NCs by raising the highest occupied molecular orbital (HOMO). The effect of aminization depends on the substituents of amines, rather than the coverage of amine-derived ligands at the NC surface. The lowest unoccupied molecular orbital (LUMO) is more sensitive to the NC size than the HOMO. Only the HOMO is sensitive to surface modification. All the aminization leads to the decrease of the HOMO–LUMO gap despite that the dominant role of quantum confinement effect is maintained in most cases. The current results contribute to the understanding of the optical behavior of Si NCs derived from the surface modification of Cl-passivated ones.