Hydrate-based CH4 storage is a promising technology for safe and economically-viable natural gas storage and transportation. Solid CH4 hydrate possesses advantages in both energy density and storage stability. The quest for an effective and economic-friendly thermodynamic promoter for CH4 hydrate formation is imminent with the aim of (a) reducing CH4 hydrate formation P-T condition and (b) increasing both the CH4 gas uptake rate and final CH4 storage capacity. In this study, a non-carcinogenic thermodynamic promoter 1,3-dioxolane (DIOX) was systematically investigated to quantify the effect of DIOX concentrations (0.15–5.56 mol%) on the process of mixed CH4 + DIOX hydrate formation. A series of thermodynamic, kinetic, Raman spectroscopy measurement, and morphology observation experiments were conducted to elucidate the mechanism of the promotion effect of DIOX at concentrations below the stoichiometric concentration (5.56 mol%). DIOX with various concentrations shifts the thermodynamic phase equilibrium of binary hydrate to the region of moderate temperature and pressure. Raman spectra provided evidence of more CH4 molecules filling in the large cages of sII hydrate with the decrease of DIOX concentration. The ratio of CH4 in large cages to CH4 in small cages of sII hydrate increases from 0.05 to 0.38 with the decrease in DIOX concentration. The gas uptake rate of CH4 declined with the decrease in DIOX concentration. We also observed that DIOX concentration is an important factor affecting the morphologies during hydrate formation. These findings provide fundamental evidence for improving the CH4 storage capacity and environmental friendliness in the application of DIOX in hydrate-based CH4 storage.