This paper presents the ionic dynamics simulation of an intermediate-temperature solid oxide fuel cell electrolyte. The example electrolyte is a yttria-doped ceria which was proved experimentally to have better performance than the traditional yttria-stabilized zirconia in the intermediate-temperature operation range below (1073 K). This paper employs the molecular dynamics technique to analyze the oxygen-ion transportation from a nanoscale aspect. The simulation reveals that the oxygen vacancy tends to be constrained near the Y3+ ions in the crystalline lattice. The influence of different operation temperatures and various Y2O3 concentrations on the ionic conductivity was studied. The results show that 10.1 mol % of Y2O3 doping concentration tends to have the optimal ionic conductivity, while the system temperature tends to increase the ionic conductivity proportionally. The simulation has been compared with published experimental data and shows reasonable agreement in both trend and order of magnitude.