To investigate the effects of Reference cement (RC) and Belite cement (LC) systems, different molecular structures of polycarboxylate ether (PCE) were prepared through the free radical polymerization reaction and designated as PC-1 and PC-2. The PCE was characterized and tested using a particle charge detector, gel permeation chromatography, a rotational rheometer, a total organic carbon analyzer, and scanning electron microscopy. The results showed that compared to PC-2, PC-1 exhibited higher charge density and better molecular structure extension, with smaller side-chain molecular weight and molecular volume. PC-1 demonstrated enhanced adsorption capacity in cement, improved initial dispersibility of cement slurry, and a reduction in slurry yield stress of more than 27.8%. LC, with its higher C2S content and smaller specific surface area compared to RC, could decrease the formation of flocculated structures, resulting in a reduction in slurry yield stress of over 57.5% and displaying favorable fluidity in cement slurry. PC-1 had a greater retarding effect on the hydration induction period of cement compared to PC-2. RC, which had a higher C3S content, could adsorb more PCE, leading to a greater retarding effect on the hydration induction period compared to LC. LC and PC-2, on the other hand, exhibited inhibition during the hydration acceleration period. The addition of PCE with different structures did not significantly affect the morphology of hydration products in the later stage, which was consistent with the trend of KDvariation. This indicates that the analysis of hydration kinetics can better reflect the final hydration morphology.