Abstract: The traditional methods for studing amino acid molecular structure are X-ray diffraction and neutron diffraction after deuteration. In this paper, X-ray diffraction, neutron powder diffraction and Raman scattering were used to study the molecular structure of alanine and leucine. Combination of infrared spectroscopy, compared with fully hydrogenated, partial deuterated and fully deuterated alanine molecules, it is shown that the traditional methods are not enough in the study of molecular structure. Meanwhile, the neutron powder diffraction method was used to measure the leucine molecule directly. It shows that neutron powder diffraction method can give the fine structure of leucine molecule.