Microwave heating is widely used to accelerate the organic synthesis reaction. However, the role of the nonthermal microwave effect in the chemical reaction has not yet been well characterized. The microwave heating processes of an ethanol-hexane mixed solution were investigated using in situ microwave irradiation nuclear magnetic resonance spectroscopy and molecular dynamics (MD) simulation. The temperature of the solution under microwave irradiation was estimated from the temperature dependence of the 1H chemical shifts (chemical shift calibrated (CSC)-temperature). The CSC-temperature increased to 58 °C for CH2 and CH3 protons, while it increased to 42 °C for OH protons during microwave irradiation. The CSC-temperature of CH2 and CH3 protons reflects the bulk temperature of solution by the thermal microwave effect. The lower CSC-temperature of the OH proton can be attributed to a nonthermal microwave effect. MD simulation revealed that electron dipole moments of OH groups ordered along the oscillated electric field decreased the entropy by absorbing microwave energy and simultaneously increased the entropy by dissipating energy to the solution as the thermal and nonthermal microwave effect. Ordered polar molecules interact to increase hydrogen bonds between OH groups as the nonthermal microwave effect, which explains the lower CSC-temperature of the OH protons. The nonthermal microwave effects contribute to the intrinsic acceleration of the organic reaction.