Water reducer and water-repellent admixture are very important in improving the workability and durability of cement-based materials. However, the synergistic effect of the two types of admixtures has not been well investigated. In this study, polycarboxylate ether-based superplasticizer (PCE) and octyltriethoxysilane (OTS) were adopted as water reducer and water-repellent admixture, respectively. Their synergistic effect on the fluidity, compressive strength, and water absorption rate of cement-based materials was investigated. Particularly, the pore structure and hydration state of cement paste were analyzed using 1H Low-Field Nuclear Magnetic Resonance (1H LF NMR). The result showed that the fluidity of cement paste containing different dosages of PCE was reduced by 5–10 mm by incorporating 1% OTS, and the compressive strength at the early age of 3 d of mortar containing high PCE dosage of 0.25% decreased up to 15% by using 1% OTS. In contrast, the compressive strength of mortar containing 0.20% PCE was slightly enhanced by the addition of 1% OTS. 1H LF NMR analysis revealed that the combination of PCE and OTS would increase the pore size and total pore volume of cement paste, and more bleeding water would be generated at high PCE dosage. The intensity-weighted T2 values of the main peak (T2¯) implied that both PCE and OTS produced a retardation effect on cement hydration. However, the water absorption rate decreased by 46.6% despite the increase in pore size and total pore volume. The conflict phenomenon powerfully revealed that the internal hydrophobic treatment by OTS has been successfully achieved. Overall, the combination of 0.20% PCE and 1% OTS exerted a positive synergistic effect in improving the compressive strength and water-repelling ability of cement-based materials, which is meaningful for improving their durability and service life.