We demonstrate the spectroscopic observation of H2 migration in the binary structure-I (sI) clathrate hydrate. The H2 molecules captured into sI small cage (sI-S) at lower temperature migrate to sI large cage (sI-L) through shared pentagonal face of 5^(12)6^(2) cage. The hexagonal faces of 5^(12)6^(2) cage provide the windows essential for creating continuous diffusion paths for H2 molecules. It is essential to realize that the vacant channels formed by the linkage of specific cages can play an important role in guest diffusion pathways and occupancy occurring in a complex clathrate hydrate matrix.