In the present study, measurements and analyses were made of the High-Power Decoupling (HPDEC) solid-state 13C NMR spectra of structure-H (sH) methane hydrates with isopentane, one of the simplest and smallest acyclic large guest molecules, and methylcyclohexane (MCH), a commonly used cyclic guest molecule that is larger than isopentane. From the spectroscopic information, clear and definite evidence for the molecular conformation of acyclic guest molecules that are sufficiently small so as to be entrapped into the structure-H large cage (sH-L) was expected. The 13C NMR chemical shift change was additionally checked through the use of a hydrogen-hydrogen steric perturbation model. From the overall results, we concluded that one of the smallest acyclic guest molecules, isopentane, participating in the formation of a structure-H clathrate hydrate is encaged, confirming the gauche conformation in large cavities. The present results strongly suggest that the guest position and structure in hydrate cages are greatly influenced by both short-range interactions between guest molecules and cage frameworks and long-range interactions between small and large guests. Accordingly, cage dynamics must be carefully considered when a specific sH hydrate is designed and synthesized for the purpose of tuning material properties.