Potassium (K) is an indispensable mineral constituent required for plant growth and many physiological processes. K deficiency and depletion in rice occurs frequently, resulting in limited growth, agronomical loss, and reduced yield. To investigate the genetics of low K (LK) tolerance, a set of high throughput genotyped chromosome segment substitution lines (CSSL) derived from the cross between Zhonghui9308 (ZH9308, susceptible to LK) and XieqingzaoB (tolerant to LK) was used to identify QTL for the shoot and root traits at the seedling stage. The experiment was conducted in hydroponic culture to explore the molecular basis of five seedling traits under two K conditions, LK and normal K (NK) and their ratio (LK/NK) for relative traits. A total of five QTL were identified on four chromosomes (3, 4, 5, and 6) with positive allelic effects from XieqingzaoB for root length (RL) and root number (RN) and negative allelic effects for shoot dry weight (SDW) and root dry weight (RDW). Two QTLs, qRN5a and qSDW4, were detected under LK and three QTLs, qRL6, qRN5b, and qRDW3, were identified under LK/NK ratio explaining 11.81% to 13.07% of total phenotypic variation. qRN5a, a novel QTL under LK, was validated in the F₂ (BC₅F₂) population and delimited to a 1023 Kb interval between the markers InD78 to RM18472. These findings will serve as important breeding material for further genetic characterization like fine mapping and cloning, which may be useful in molecular marker-assisted breeding.