The objective of the research was to study the correlations between near infrared spectra and molecular structures of 20 standard amino acids. It was to establish the theoretical foundation for widely use of the amino acids near infrared spectra in animal science, food and medicine. Measurement of the near infrared spectra was performed using a Shimadzu Fourier transform infrared spectrophotometer IRPrestige-21, with FlexIRTM Near-Infrared Fiber Optics module. The spectrometric data acquisitions were performed by Shimadzu IRsolution 1.50 system. The spectrometric room temperature was 25 ℃ and humidity was 38%. Spectra of 20 amino acid standard substances were collected by reflectance mode from 1 000 to 2 502 nm in 8 cm-1 increment. Each sample was scanned in three times, each scan was 50 cycles, and the average value of three times scan result was used for each sample. Based on the differences of amino acids side chains, the correlations between near infrared spectra and molecular structures were compared in the fat family amino acids, aromatic amino acids and heterocycle amino acids. The result shows that all 20 standard amino acids have very specific absorption line patterns. It is distinctly different in these absorption line patterns. Near-infrared spectra of high molecular weight fat family amino acids are affected by side chains. Near-infrared spectra of glycine are affected by carboxyl and amino. The differences of near-infrared spectra between two aromatic amino acids are in benzene ring. —OH groups on benzene ring of tyrosine lower the symmetry of benzene molecule. It leads to the emergence of more vibration absorption. Near-infrared spectra of heterocycle amino acids are distinctly different in 1 000～2 502 nm because of side chains. In conclusion, there are four different characteristic spectral regions. The first one is 1 050～1 200 nm spectral region which is composed mainly of second-order frequency doubling of C—H group. The second is 1 300～1 500 nm spectral region which is composed mainly of combination tune of C—H group. Due to side chains of amino acid have different molecular structure, they yield a complete set of near infrared fingerprint spectra between 1 600～1 850 and 2 000～2 502 nm. In another words, these four characteristic regions of near infrared spectra can be used to build the model of qualitative analysis and quantitative analysis for amino acid, and improves the accuracy and reliability of model.