Deep understanding of slow-wilting is essential for developing drought-tolerant crops. Existing approaches to measure transpiration rates are difficult to apply to large populations due to their high cost and low throughput. To overcome these challenges, we developed a high-throughput phenotyping system that integrates a load cell sensor and an Arduino-based microcontroller device. The system tracked the transpiration rate in real time by measuring changes in the pot weight in 224 recombinant inbred lines of Taekwangkong (fast-wilting) x SS2-2 (slow-wilting) under water-restricted conditions. Among five transpiration features we determined, stress recognition time point (SRTP) and decrease in transpiration rate by stress (DTrs) are informative parameters, that are interconnected and independently affect slow-wilting as well. Quantitative trait loci (QTL) for SRTP and DTrs were identified at the same location as the major QTL for slow wilting, <i>qSW_Gm10</i>, identified in the previous study. Notably, we found a novel major QTL for DTrs, <i>qDTrs_Gm04</i>, with a LOD value of 42 and PVE of 47 ​%. As a candidate gene for <i>qDTrs_Gm04</i>, <i>GmWRKY58</i> was selected with differential expression between the parental lines under drought conditions as well as upstream sequence variation. Our high-throughput system is of help not only to biological research but breeding programs of drought-tolerant lines.