<p>Solid Oxide Fuel Cells (SOFCs) are high-efficiency clean cogeneration devices. Accurately characterizing the complex coupling characteristics of heterogeneous energy between the stack and external auxiliary systems is critical for enhancing SOFC energy conversion efficiency. This study integrates heat transfer, mass transfer, and electrochemical processes into a unified energy circuit through standardized thermal resistance and equivalent circuit methods, establishing a cross-scale integrated power flow model for SOFCs. Furthermore, by combining the standard thermal resistance-based entropy generation rate formulation with traditional exergy analysis, parameter interactions and coupling mechanisms can be analyzed without introducing non-device-specific variables. Building upon this foundation, a comprehensive analysis was conducted to evaluate the impacts of SOFC structural and operational parameter variations on both energy and exergy efficiencies. The results demonstrate that increasing the thermal conductivity of the air preheater in the waste heat recovery system yields the most significant improvement in thermal recovery efficiency, achieving a 9% enhancement. Enhancing the waste heat exchanger’s thermal conductivity achieves the highest overall system efficiency improvement rate of 1.275%/(kW·K⁻¹). Increasing the thermal conductivity of the steam generator can achieve the maximum system exergy efficiency increase rate of 1.1%/(kW·K⁻¹). When the water-to-carbon ratio increases from 2 to 4, both stack power generation efficiency and heating efficiency decrease, resulting in a 13.8% reduction in total system efficiency. Increasing the air excess ratio from 1.5 to 3.5 decreases stack efficiency but increases heating efficiency, leading to a net 16.9% total system efficiency reduction. The proposed modeling approach ultimately provides an accurate and efficient analytical tool for enhancing SOFC’s integrated energy utilization efficiency.</p>