In a microwave field, the dielectric properties, molecular structures, and hydrogen bonding dynamics of glycerol in its mixtures with water were determined by the molecular dynamics simulation method. The dipole–dipole correlation of glycerol is linked to the field intensity of microwaves. The results show that as the field intensity is increased, even glycerol in the second coordination shell can become correlated with each other. The structures of up to 35 glycerol molecules are observed. More than that, it was observed that lifetimes of glycerol–glycerol hydrogen bonds were prolonged, while the average hydrogen bond number was also increased. Besides, the structures in a strong microwave field mimic the weak C–H⋯O hydrogen bonds seen in high-glycerol concentration mixtures, yet the concentration is lower. These results indicate that with the assistance of the microwave field, glycerol molecules become concentrated and are more likely to establish stable interactions with others. As a consequence, the spherical clusters composed by glycerol molecules in our nanosheet synthesis experiment are easier to form.