Grinding aids (GAs) are an important addtive in the cement production process. However, the relationship between the molecular structure of GAs and its grinding efficiency has not been clearly revealed. In this study, the influence of GAs with different structures, including glycols and alkanolamines, on the grinding efficiency of pure clinker was systematically investigated. The working mechanism from their adsorption and dispersion configurations on tricalcium silicate (C3S) surface was investigated by first-principles method. As the structural parameters of GAs, number of polar groups is found to affect the grinding efficiency of cement clinker. The grinding performance of alkanolamines is better than that of glycols at the same dosage, when the number of hydroxyl groups is the same. The tertiary alkanolamines are adsorbed through the double-ended hydroxyl group to form larger molecular projection areas than the glycols with single-ended hydroxyl group, thus resulting in higher dispersion efficiency. Further, with the growth of the number of methyl groups in the molecular structure of the tertiary alkanolamines, the thickness of the adsorbed molecular layer grows from 9.25 Å to 9.87 Å, and the ability to shield the electrostatic forces between cement particles is enhanced and result in a better grinding aid performance.