Understanding the electrode properties at the atomistic level is of great benefit to the evaluation of electrode performance and design of better electrode materials in solid oxide fuel cells. In this work, density functional theory (DFT) calculations are employed to investigate the formation and conducting behaviors of oxygen vacancies and proton defects in Ruddlesden-Popper oxide SrEu2Fe2O7 (SEFO), which has been experimentally characterized as a promising cathode. The calculation results suggest both oxygen vacancies and proton defects can be formed in SEFO, and especially, the formation of these defects is largely dependent on oxygen sites in the special crystal structure with alternative stacking of rock-salt layers and double-layered perovskite slabs. The oxygen vacancies within the perovskite slabs have very low formation energies, but demonstrate high energy barriers for migration and low hydration properties; while in the case of those in the rock salt layers, it's contrary. Interestingly, protons have similar migration abilities in the perovskite slabs and rock salt layers. And therefore, increasing the vacancy concentration of the rock salt layer is beneficial to increase the concentration of proton defects and to improve the proton conductivity. DFT calculations also indicate that substituting Zn for Fe in SEFO can largely depress the oxygen vacancy formation energy, which helps to increase the concentration of both defects. Importantly, the energy barriers for migration of both oxygen ions and protons are barely enhanced, implying a negligible trapping effect of the Zn dopant.