The deformation mechanism of a polymer crystal has been directly clarified for the first time using an imaging-plate X-ray structural analysis system for a polydiacetylene single crystal subjected to a tensile stress at room temperature as well as at 122 K. That is to say, the small displacements of the constituent atoms of the planar-zigzag skeletal chain could be successfully detected. The change in the internal coordinates such as bond length and bond angle, which were induced by tensile stress, has been found to be consistent with the previously reported lattice-dynamical prediction. This first success in the accurate structural analysis of the deformed polymer crystal is considered to supply a new technique for investigating the deformation mechanism of polymer materials from the molecular level.