The conformations of (pentafluorophenyl)propyl groups (-CH2-CH2-CH2-C6F5, abbreviated as PFP), covalently bound to the surface of mesoporous silica nanoparticles (MSNs), were determined by solid-state NMR spectroscopy and further refined by theoretical modeling. Two types of PFP groups were described, including molecules in the prone position with the perfluorinated aromatic rings located above the siloxane bridges (PFP-p) and the PFP groups denoted as upright (PFP-u), whose aromatic rings do not interact with the silica surface. Two-dimensional (2D) C-13-H-1, C-13-F-19 and F-19-Si-29 heteronuclear correlation (HETCOR) spectra were obtained with high sensitivity on natural abundance samples using fast magic angle spinning (MAS), indirect detection of low-gamma nuclei and signal enhancement by Carr-Purcell-Meiboom-Gill (CPMG) spin-echo sequence. 2D double-quantum (DO) F-19 MAS NMR spectra and spin echo measurements provided additional information about the structure and mobility of the pentafluorophenyl rings. Optimization of the PFP geometry, as well as calculations of the interaction energies and F-19 chemical shifts, proved very useful in refining the structural features of PFP-p and PFP-u functional groups on the silica surface. The prospects of using the PFP-functionalized surface to modify its properties (e.g., the interaction with solvents, especially water) and design new types of the heterogeneous catalytic system are discussed.