A low thermal scanner has been completely developed for improving DC voltage calibration from semi-automatic to fully automatic measurement system. The application of the switching system inside the built-up scanner introduced offset voltage to the measurement due to thermal electromotive force (EMF). A differential measurement method was proposed to characterize the thermal EMF of the scanner, and this method has been compared to previous characterization using the direct measurement method. The results show that the differential measurement method could minimize the thermal EMF effect, and the thermal EMF had a negligible contribution to the measurement for uncertainty levels around 10 to 11 ppm. Therefore, the differential measurement method is recommended for DC voltage calibration with uncertainty levels below 10 ppm since the thermal EMF can significantly affect the measurement. Furthermore, the direct measurement method is suggested for DC voltage calibration with uncertainty levels above 11 ppm since it can speed up the measurement process.