The thermal-electric conversion efficiency is a crucial metric for evaluating the performance of a thermoelectric generator (TEG). However, accurate measurement of this efficiency remains a significant challenge due to various factors that impact heat flow measurements. We have observed that temperature fluctuations during temperature control are the primary factor contributing to measurement errors in heat flow under vacuum conditions. To address this issue, we have developed a time-dependent theoretical model for the thermal-electric coupling of a TEG measurement system based on Fourier’s theory of heat conduction. This model allows us to investigate the effects of both temperature fluctuation and structural parameters on the measurement error of TEG performance. Furthermore, we have proposed an error correction scheme for TEG performance based on our theoretical and experimental findings. These insights provide a theoretical framework and technical guidance for more precise measurements of TEG performance.