Antimicrobial peptides (AMPs), due to their unique structure/function relationship, have great opportunities to be developed into novel diagnostic and therapeutic agents for a variety of pathogens and illnesses. Often such peptides are administered using powder or suspension, limiting their reusability or recyclability. Immobilization of these antimicrobial peptides on biotic/abiotic surfaces may circumvent such disadvantages, but such immobilization is likely to not only change the peptide secondary structures and their orientations but also ultimately affect functionality. In order to better understand surface-bound structures of AMPs on abiotic surfaces, cecropin A (1–8)–melittin (1–18) hybrid peptides were chemically immobilized on polymer surfaces prepared by chemical vapor deposition (CVD) polymerization. Measurements by sum frequency generation (SFG) vibrational spectroscopy and circular dichroism were used to characterize the peptides immobilized on the CVD-based polymer in situ. In addition, coarse-grained molecular dynamics (MD) simulations were used to understand the orientation of these peptides on the molecular level. Simulation results were highly consistent with experimental data. Results indicated that, unlike other linear peptides immobilized on similar abiotic surfaces, this hybrid peptide immobilized on CVD-based polymer surfaces exhibited two bending points. Such conclusions help further understand the role surface immobilization for such unique molecules.