Limestone method is widely used in FGD process because of high desulfurization efficiency and low cost. However, it is easy to precipitate and block the equipment because of large particle size. Thus, micron CaCO3 slurry and CaCO3 (30- and 100-nm diameter) nanofluids of the same concentrations were prepared to investigate the influence of the particle size on suspension of absorbent and the desulfurization effect. Settlement experiment and zeta potential (ζ) measurements depicted that the stability of CaCO3 nanofluids were much better than that of micron CaCO3 slurry, which could avoid the blocking of equipment. Moreover, the viscosity of CaCO3 nanofluids was directly proportional to concentration and inversely proportional to temperature. Dynamic viscosity of two types of CaCO3 nanofluids decreased first and then remained unchanged with the shear rate varying from 0 to 1000 s−1 while the viscosity of CaCO3 (30-nm-diameter) nanofluids was higher than that of CaCO3 (100-nm-diameter) nanofluids. Dynamic absorption experiments indicated that the desulfurization effect of two kinds CaCO3 nanofluids were better than that of micron CaCO3 slurry. While the maximum saturated sulfur content of CaCO3 (100-nm-diameter) nanofluids could be 54.38 mg/mL and the maximum breakthrough time was 300 minutes, which was higher than CaCO3 (30-nm-diameter) nanofluids. The maximum mass transfer rate of CaCO3 (100-nm-diameter) nanofluids could be 2.523 m/s, which was consistent with the desulfurization experiment. Hence, properly reducing the particle size of CaCO3 particles can improve the desulfurizing effect on the premise of not increasing the viscosity of desulfurizing solvent. Novelty Statement The manuscript "An investigation into the influence mechanism of particle size of CaCO3 on FGD process by limestone method" reduced the particle size of CaCO3 in limestone method from micron to nanometer for the first time. The stability and rheology of high concentration CaCO3 (30- and 100-nm in diameter) nanofluid were studied. It also found that properly reducing the particle size of CaCO3 particles could improve the desulfurizing effect on the premise of not increasing the viscosity of desulfurizing solvent.