A novel peptide-based three-dimensional probe called "peptide matrix," inspired by the antibody paratope region, was fabricated on a surface plasmon resonance (SPR) sensor chip to enhance the sensitivity of detecting the explosive 2,4,6-trinitrotoluene (TNT). Although peptide aptamer is an attractive candidate for a molecular recognition probe because of its ease of synthesis and chemical stability, it still has difficulty in applying to highly sensitive (i.e. parts-per-billion (ppb) or sub-ppb level) detections. Thus, we developed the concept of peptide matrix structure, which is constructed by consecutive disulfide bond formation between a large number of peptide fragments. This robust three-dimensional structure displays multiple binding sites which can efficiently associate with each TNT molecule. The peptide matrix lowered the dissociation constant (KD) by two orders of magnitude compared to the linear peptide aptamer, estimating KD as 10.1 nM, which is the lowest concentration reported by using peptide-based TNT probe. Furthermore, the concentration limit of detection of peptide matrix modified SPR sensor was 0.62 ppb, and hence comparable to single-chain variable fragment (scFv)-based TNT sensors. To our knowledge, this is the first report demonstrating peptide matrix fabrication and its application for small explosive molecule detection. This peptide matrix-based approach, which has the advantage of simple synthesis and high sensitivity, will be applicable to many other small-molecule label-free detections.