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Cold stress in rice is a critical factor limiting growth and yield in temperate regions. In this study, we identified quantitative trait loci (QTL) conferring cold tolerance during the booting stage using a recombinant inbred line population derived from a cross between a cold-susceptible Tongil-type cultivar Milyang23 and a cold-tolerant <i>japonica</i> cultivar Giho. A phenotypic evaluation was performed in a cold-water-irrigated field (17 °C) and a temperature-controlled (17 °C/17 °C air and water) greenhouse at the booting stage. Four QTL, including two on chromosome 1 and one each on chromosomes 6 and 9, were identified in the cold-water-irrigated field, with an R² range of 6.3%–10.6%. Three QTL, one on each of chromosomes 2, 6 and 9, were identified under the temperature-controlled greenhouse condition, with an R² range of 5.7%–15.1%. Among these, two QTL pairs on chromosomes 6 (<i>qSFF6</i> and <i>qSFG6</i>) and 9 (<i>qSFF9</i> and <i>qSFG9</i>) were detected in the cold treatments of both field and greenhouse screenings. Our results provide a reliable dual-screening strategy for rice cold tolerance at the booting stage.