Mordenite has one-dimensional 8-ring and 12-ring channels running parallel to the c-axis and Se molecules were successfully incorporated into the mordenite channels through a vapor phase after dehydration. The structure of the Se-incorporated mordenite was analyzed by single crystal X-ray diffraction coupled with anomalous X-ray scattering (AXS). The AXS analysis confirmed the Se distribution in the 12-ring channels only, by analyzing the intensity contrast observed at the Se K-absorption edge. And this environmental structure information allows us to improve the structural analysis of the ordinary single crystal X-ray diffraction. The present analysis suggested that Se molecules such as an infinite chain and its fragments were preferentially formed in the 12-ring channels together with the feasible bonding of Se-Na pairs. The location and probability of Na in the 12-ring channels are suggested to be considered as important factors affecting the probability of Se chain and its fragmentation.