The superior optical properties of Silicon Quantum Dots (SQDs) have made them of increasing interest for a variety of biological and opto-electronic applications. The surface functionalization of the SQDs with aromatic ligands plays a key role in controlling their optical properties due to the interaction of the ligands with the electronic wave function of SQDs. However, there is limited reports in literature describing the impact of spacer groups connecting the aromatic chromophore to SQDs on the optical properties of the SQDs. Herein, we report the synthesis of two SQDs assemblies (1.6 nm average diameter) functionalized with perylene-3,4,9,10-tetracarboxylic acid diimide (PDI) chromophore through N-propylurea and propylamine spacers. Depending on the nature of the spacer, the photophysical measurements provide clear evidence for efficient energy and/or electron transfer between the SQDs and PDI. Energy transfer was confirmed to be the operative process when propylurea spacer was used, in which the rate was estimated to be ~2 × 109 s−1. On the other hand, the propylamine spacer was found to facilitate electron transfer process within the SQDs assembly. To illustrate functionality, the water soluble SQD-N-propylurea-PDI assembly was proven to be nontoxic and efficient for fluorescent imaging of embryonic kidney HEK293 cells and human bone cancerous U2OS cells.