We aimed to develop an amino acid sequence-dependent analytical method using near-infrared (NIR) spectroscopy. The detailed analysis of the NIR spectra of eight different amino acid aqueous solutions (glycine, alanine, serine, glutamine, lysine, phenylalanine, tyrosine, and proline) revealed different spectral patterns characteristic of different amino acid residues in the 6200-5700 and 5000-4200 cm-1 regions, and the amino acids were identified based on the patterns. The spectra in the region of 5000-4500 cm-1 for tripeptide organic solutions that were composed of the aforementioned eight amino acids clearly showed the spectral differences depending on the amino acid species and amino acid sequences. Namely, tripeptide species were clearly differentiated from each other based on the spectral pattern of NIR bands due to the combinations of N-H stretching and amide II/III modes and those derived from the first overtones of amide II and amide I. The quantitative evaluation of changes in the concentrations of dipeptides and tripeptides composed of two different amino acids, glycine and proline was performed using partial least squares regression (PLSR) analysis and a combination of bands for amide modes. The calibration and validation results with high determination coefficients (R2 ≥ 0.99) were successfully obtained based on the amino acid sequences. The results not only revealed the usefulness of NIR spectroscopy as a process analytical technology (PAT) tool for synthesizing peptides in a micro flow reactor but also proposed a general method for quantitatively analyzing NIR spectra obtained in the course of chemical synthesis.