It has been reported that some aldehyde compounds have formed simple sII clathrate hydrates without help-gas molecules, showing a self-forming effect. However, the structure of aldehyde hydrates is quite unstable due to the “gem-diol reaction”. According to the previous studies, the aldehyde hydrate slowly decomposes at atmospheric condition with the conversion of aldehyde to gem-diol. We investigated binary aldehyde (acetaldehyde, propionaldehyde, and isobutyraldehyde)+methane clathrate hydrate with spectroscopic and thermodynamic analyses. Similar to the simple aldehyde hydrate, the binary hydrates also formed a sII hydrate. During the hydrate formation process, we found that most of the aldehydes converted to gem-diols and were then incorporated into the large cages of the sII hydrate. Depending on the equilibrium constant of the gem-diol reaction caused by the molecular structures of the three aldehydes, different phase equilibrium curves of aldehyde+methane hydrates were obtained.