Peptide-modified delivery systems are enabling the improvement of the targeting specificity, biocompatibility, stability, etc. However, the precise design of a peptide-decorated surface for a designated function has remained to be challenging due to a lack of mechanistic understanding of the interactions between surface-bound peptide ligands and their receptors. Enlightened by the recent report on pairwise interactions between peptides in the solution state and surface-immobilized state, we used computational simulations to explore the contributing mechanisms underlining the observed binding affinity characteristics. Molecular dynamics simulations were performed to sample and compare conformations of homo-octapeptides free in solution (mobile peptides) and bound to the surface (N-terminal fixed peptides). We found that peptides converged to more extended and rigid conformations when immobilized to the surface and confirmed that the extended structures could increase the space available to counter-interacting peptides during the peptide–peptide interactions. In addition, studies on interactions between stationary and mobile peptides revealed that main-chain/side-chain and side-chain/side-chain hydrogen bonds play an important role. The presented efforts in this work may provide supportive references for peptide design and modification on the nanoparticle surface as well as guidance for analyzing peptide–receptor interactions through an emphasis on hydrogen bonds during peptide design and an understanding of the influence on the binding affinity by the sequence-dependant conformational changes after peptide immobilization.