The rice cultivar ‘Chamdongjin’ exhibits a distinctively large grain size and excellent eating quality but is weak with regard to pre-harvest sprouting (PHS), requiring genetic improvement. In contrast, the premium-quality rice cultivar ‘Younghojinmi’ exhibits strong PHS tolerance. This study conducted quantitative trait loci (QTL) analysis on PHS and low-temperature germinability (LTG) using recombinant inbred lines derived from a cross between ‘Chamdongjin’ and ‘Younghojinmi’ to elucidate the genetic factors. Thus, an elite line with improved PHS tolerance was selected. QTL analysis revealed that qPHS3 and qLTG3 were associated with PHS and LTG, respectively, and the candidate gene was identified as qLTG3-1. The loss-of-function allele qltg3-1 in ‘Younghojinmi’ enhanced PHS tolerance compared to the functional allele qLTG3-1 in ‘Chamdongjin,’ but it also showed a trade-off relationship by decreasing LTG. CY_RILs carrying qltg3-1 exhibited lower PHS and LTG rates of 17.9% and 41.6%, respectively, compared to 44.1% and 55.7%, respectively, for CY_RILs with qLTG3-1. The elite line, CY_RIL79, carrying qltg3-1, was selected from CY_RIL. This line was recognized for its PHS tolerance while maintaining the key agricultural traits of ‘Chamdongjin,’ thus designated ‘Jeonju697.’ ‘Jeonju697’ is expected to be utilized as a practical alternative for addressing the issue of enhancing PHS tolerance in ‘Chamdongjin’; however, considering its weak LTG, it is desirable to improve this trait through further breeding efforts.