Clay often has severe detrimental impacts on cement-based materials. Therefore, it is necessary to investigate the mechanism causing the deterioration to improve the service life of cement-based materials. Based on accurate dimensional analysis, a mechanism that influences clay is proposed: the intercalation of the side chains of superplasticizer molecules in the interlayer space of the clay. To lessen this harmful effect, a new clay-resistant admixture (CRA) possessing cationic groups of small molecular size was synthesized through a novel dimensional design. The length and width of the side chains of this superplasticizer molecule were 9.50–17.50 and 0.25–0.40 nm, respectively, with a radius of ~3.74 nm in solvent, which is larger than the interlayer spacing of montmorillonite (i.e. 1.09–2.14 nm). The longitudinal and latitudinal lengths of the CRA molecule were 0.468 and 9.456 nm, respectively, ensuring intercalation in the interlayer of montmorillonite. The increase in interlayer spacing of the clay was 0.364 nm following addition of polycarboxylate superplasticizer (PCE) plus CRA and 0.632 nm following addition of PCE, which suggests that the CRA plays the role of a ‘sacrificial agent’ that is preferentially intercalated into the interlayer space of clay to further prevent the side chains of the superplasticizer molecules from entering the interlayer. The aim of this study was to propose a suitable means of synthesizing a new CRA to address the impact of clay through dimensional design and mechanism analysis, which contributes to the theoretical study and technological improvement of cement-based materials.