Ammonia is a carbon-free energy vector and has attracted great attention toward “zero-carbon emission” and “energy N-cycle” in the futuristic energy system. In this work, we applied perovskite SrTiO3 oxides as anode catalysts in NH3-fed solid oxide fuel cells (NH3-SOFCs) and investigated the effects of cation-deficient A sites and Ni-doped B sites on the conductivity and band structure by a series of characterizations. The results showed that appropriate A-site-deficient Sr0.9Ti1-yNiyO3-δ oxides as anodes improve the electrochemical performance in the NH3-SOFCs, while a negative effect was found for the B-site-deficient cases. Instead, the low valence Ni2+ arranged at B sites of Sr0.9TiO3-δ promote the reduction of Ti4+ to Ti3+, generating oxygen vacancies and then facilitating the electron migration in the reaction. Benefited from the ex-solution of Ni nanoparticles (NPs), the optimal powder density of the NH3-SOFC by electrolyte-supported YSZ is obtained over the Sr0.9Ti0.8Ni0.2O3-δ (STN0.2), reaching 287.1 and 262.7 mW·cm−2 in H2 and NH3 at 800 °C, respectively, presenting a high utilization rate of NH3. The activity of STN0.2 is 1.5-fold higher than that of NH3-SOFC adopting NiO/YSZ anode under the same conditions. The excellent electrochemical performance of STN0.2 is attributed to small flat-band potential, conduction band, band gap and high conductivity, resulting in a feasible bound electron transition to free electron. Combining distribution of relaxation time and the Bode plots analysis, we propose the preferential reaction mechanism and rate determining step.