Polycarboxylate superplasticizer (PCE) is a widely used water-reducing agent that can reduce significantly the water demand of concrete, which reduces the porosity and enhances the strength and durability of the concrete. (The PCE consists of a single backbone with many long PEO side chains.) Generally, aggregate occupies >70 wt.% of concrete; clay minerals are ubiquitous in nature and are difficult to avoid in mined aggregates. Clay minerals in aggregate often render the PCE ineffective and give rise to rapid loss of the fluidity of the concrete; this phenomenon is referred to as ‘poor clay tolerance of PCE.’ Though the poor clay tolerance of PCE is known widely, the relationship between the clay tolerance and the molecular structure of the PCE, in particular the effect of the side-chain structures, on clay tolerance is not understood completely. The objective of the present study was to determine the effect of different grafting densities of polyethylene oxide (PEO) side chains on the clay tolerance of PCE. The raw materials included mainly PCE, which was synthesized using acrylic acid and isopentenol polyoxyethylene ether, and a natural montmorillonite (Mnt), one of the most common clay minerals. The loss of fluidity of the cement paste was tested to assess the clay tolerance; total organic carbon was used to measure the amount of PCE adsorbed; X-ray diffraction, transmission electron microscopy, Fourier-transform infrared spectroscopy, and thermogravimetric analysis were used to investigate the microstructure of the intercalated Mnt. The results showed that preventing the superficially adsorbed PCE from being intercalated into Mnt was of great importance in terms of the improvement in clay tolerance of PCE, which increased with greater grafting density of PEO in the side chain of the PCE. The results also suggested the possibility that polymers which intercalate preferentially into the Mnt could improve significantly the clay tolerance of the PCE system.