Sulfur dots are a new class of recently developed nonmetallic luminescent nanomaterials with various potential applications. Herein, we synthesized sulfur dots using a mild chemical etching method and then modified the structural features of the assynthesized sulfur dots using a slow and defined solvent-assisted aggregation process. This increases the particle size and overall crystallinity along with the modifications of the surface functional groups, which eventually show a new emission band at longer wavelengths. Detailed photophysical and temperature-dependent luminescence studies confirmed that the new emissive state evolves due to interparticle interactions in the excited state. Furthermore, the occurrence of a new emissive state in a longer-wavelength region helped reduce the energy gap between the lowest excited singlet state and the lowest excited triplet state in modified sulfur dots, resulting in an aqueous stable room-temperature phosphorescence/ afterglow emission through efficient intersystem crossing. This typical efficacious afterglow emission directly shows the potential applicability of structurally modified sulfur dots in encryption devices and can also be potentially effective in light emitting diodes (LED) and sensing devices.