The crystal structure of polydiacetylene giant single crystal has been analyzed on the basis of the two different methods of wide-angle neutron diffraction and X-ray diffraction. The X-ray result gives us the total electron density distribution [rho(x)] of polymer chain. The neutron result tells the positions of atomic nuclei, which can allow us to speculate the electron density distributions [rho(0)(x)] around the nonbonded isolated atoms. As a result, the so-called bonded (or deformed) electron density Delta rho(x) [(math) rho(x) = rho(0)(x) - p(x)(x) - rho(N)(x)], i.e., the electron density distribution due to the conjugation among the covalently bonded atoms along the polymer chain, can be estimated using the two information obtained by the X-ray and neutron data analyses (the so-called X-ray-neutron subtraction (X-N) method). The present report is the first example of the application of X-N method to the synthetic polymer species. The Delta rho(x) derived for polydiacetylene was found similar to that of the low-molecular-weight model compound having the similar electronically conjugated chemical formula. The Delta rho(x) was calculated by the density functional theory, which was in a good agreement with the experimental result qualitatively.