Lipopolysaccharide (LPS) is a component of the outer membrane of Gram-negative bacteria. Recently, a label-free immobilized antimicrobial peptide (AMP) surface plasmon resonance platform was developed to successfully distinguish LPS from multiple bacterial strains. Among the tested AMPs, SMAP29 exhibited excellent affinity with LPS and has two independent LPS-binding sites located at two termini of the peptide. In this study, sum frequency generation vibrational spectroscopy was applied to investigate molecular interactions between three LPS samples and surface-immobilized SMAP29 via the N-terminus, the C-terminus, and a middle site at the solid/liquid interface in situ in real-time, supplemented by circular dichroism spectroscopy. It was found that the conformations and orientations of surface-immobilized SMAP29 via different sites are different when interacting with the same LPS, with different interaction kinetics. The same SMAP29 sample also has different structures and interaction kinetics while interacting with different LPS samples with different charge densities and hydrophobicities. The observed results on molecular interactions between surface-immobilized peptides and LPS can well interpret the different adsorption amounts of various LPSs on different surface-immobilized peptides.