Traditional Yttria Stabilized Zirconia (YSZ) for the solid oxide fuel cell (SOFC) is not suitable for the low temperature operation. The ionic conductivity of the electrolyte decreases dramatically when the operation temperature is below 650°C. This paper intends to replace it by a new Yttria doped Cerium (YDC). A nano scale analysis was performed beforehand to simulate the oxygen ion transfer inside the electrolyte by the molecular dynamics (MD) technique. Simulation results showed that the hopping migration of oxygen ions dominates the transfer process instead of continuous diffusion. Different doping concentrations of Yttria showed strong influence to the ionic conductivity and an optimal value of 10 mole% was found by this simulation technique. The MD simulations of both YSZ and YDC were carried out at different operating conditions. They were compared with published experimental data and showed good agreements. The conclusion is reached that the YDC has potential to replace the traditional YSZ and further promotes the performance of the SOFCs.