The primary development strategy for ammonia-fueled solid oxide fuel cell (SOFC) focuses on enhancing the cell lifetime by reducing the operating temperature, albeit inevitably affecting the cell output performance. This study has established a multi-physics model of the single ammonia-fueled tubular SOFC and conducted a thorough analysis and weighing of the improvements in cell stress and the losses in output performance at low temperature operating conditions. As the operating temperature is reduced from 800 °C to 700 °C, the inhomogeneity in its internal temperature distribution and stress distribution is significantly reduced, albeit with a concomitant increase in ohmic impedance by 1.75 Ω cm2 and a reduction in maximum power density by 42.16 %. The study employs the reduction of electrolyte thickness to compensate for the ohmic losses incurred by low temperature, while simultaneously incorporating a material thermal deformation constraint mechanism. As the electrolyte thickness is reduced from 200 μm to 20 μm, the overall thermal deformation variance ranges from 0.0977 to 0.1214. When the electrolyte thickness falls below 80 μm, there is a significant increase in thermal deformation variance. However, adjusting the electrolyte thickness within the range of 80–200 μm results in a relatively small change in overall thermal deformation variance, while also achieving a power density improvement of 0–30.57 %.