We investigated for the first time the abnormal thermal expansion induced by an asymmetric guest structure using high-resolution neutron powder diffraction. Three dihydrogen molecules (H2, D2, and HD) were tested to explore the guest dynamics and thermal behavior of hydrogen-doped clathrate hydrates. We confirmed the restricted spatial distribution and doughnut-like motion of the HD guest in the center of anisotropic sII-S (sII-S=small cages of structure II hydrates). However, we failed to observe a mass-dependent relationship when comparing D2 with HD. The use of asymmetric guest molecules can significantly contribute to tuning the cage dimension and thus can improve the stable inclusion of small gaseous molecules in confined cages.