The complex phase behaviors and structural coexistence of natural gas hydrates (NGHs) that contain large-molecule guest substances (LMGSs) were examined for their significance in the exploration and exploitation of NGHs as well as natural gas storage and transportation. Methylcyclopentane (MCP) and 2,2-dimethylbutane [neohexane (NH)] were chosen as LMGSs, and the simplest composition of NGHs and natural gas was simulated by a gas mixture of CH4 (90%) + C2H6 (10%). The coexistence of structure II (sII) and structure H (sH) hydrates in the CH4 + C2H6 + LMGS + water mixtures was revealed by C-13 nuclear magnetic resonance (NMR) and powder X-ray diffraction (PXRD). CH4 and LMGSs were captured in sH, whereas CH4 and C2H6 were enclathrated in sII. Endothermic heat flow curves, which were obtained by a differential scanning calorimeter (DSC), and pressure (P)-temperature (T) traces exhibited two-step dissociation of formed gas hydrates (sH dissociation followed by sII dissociation). The experimental results for the PXRD patterns, C-13 NMR spectra, phase equilibria, DSC heating curves, and P-T traces clearly demonstrated that the CH4 (90%) + C2H6 (10%) + LMGS + water mixtures formed both sII hydrates and sH hydrates and that the final hydrate structure at equilibrium dissociation points was sII.