Cationic nanoparticles are known to interact with biological membranes and often cause serious membrane damage. Therefore, it is important to understand the molecular mechanism for such interactions and the factors that impact the degree of membrane damage. Previously, we have demonstrated that spatial distribution of molecular charge at cationic nanoparticle surfaces plays an important role in determining the cellular uptake and membrane damage of these nanoparticles. In this work, using diamond nanoparticles (DNPs) functionalized with five different amine-based surface ligands and small phospholipid unilamellar vesicles (SUVs), we further investigate how chemical features and conformational flexibility of surface ligands impact nanoparticle/membrane interactions. 31P-NMR T2 relaxation measurements quantify the mobility changes in lipid dynamics upon exposing the SUVs to functional DNPs, and coarse-grained molecular dynamics simulations further elucidate molecular details for the different modes of DNP-SUV interactions depending on the surface ligands. Collectively, our results show that the length of the hydrophobic segment and conformational flexibility of surface ligands are two key factors that dictate the degree of membrane damage by the DNP, while the amount of surface charge alone is not predictive of the strength of interaction.