Detailed investigation of macroscopic deformation and nanoscopic structural changes in flexible organic crystals pose challenges for investigators. Herein, applied stress and subsequent relaxation of elastic organic crystals resulted in reversible macroscopic crystal deformation. X-ray diffraction with a curved jig revealed reversible nanoscopic structural changes in the crystal structure under the bending stress and relaxation. The crystal lattice changed quantitatively under the applied macroscopic stress-strain (%). This method enables quantitative monitoring of the dynamic nanoscopic structural changes in detail associated with crystal deformation through the use of standard laboratory X-ray diffraction analysis. Importantly, the developed method offers a way of quantitatively measuring reversible structural changes, without synchrotron X-ray analysis. Moreover, the analysis derives Poisson’s ratio, i.e., the ratio of the change in the width per unit width of materials. It is important in materials science, normally has a positive value in the range of 0.2–0.5. However, the crystals show not only the "Poisson effect" but also the unusual "negative Poisson effect". This novel approach for investigation generates unprecedented opportunities for understanding dynamic nanostructure changes in flexible organic crystals.