‘Koshihikari’ is a high-quality japonica rice cultivar from Japan, exhibiting a medium-early heading type under Korean conditions, with tall plant height and susceptibility to lodging. ‘IS592BB’ is an early-maturing japonica rice cultivar in Korea, characterized by short culm, lodging tolerance, and multiple disease resistance. In this study, a recombinant inbred line population derived from a cross between ‘Koshihikari’ and ‘IS592BB’ (KSIS_RIL) was developed to investigate the genetic basis of heading date (HD) and yield-related traits through QTL analysis. QTLs associated with HD were identified on chromosomes 3, 6, and 8, and the candidate genes were assigned as Hd1 (Heading date 1), Hd16, Hd17, and Hd18. Among these, Hd1 was identified as the major QTL with the largest effect on HD variation and exhibited pleiotropic effects on multiple yield-related traits, including culm length (CL), panicle length (PL), number of spikelets per panicle (NS), ratio of ripened grain (RRG), brown/rough rice ratio (BRR), and grain yield per plant. Hd17 also affected HD, NS, and 1,000-grain weight (TGW), whereas Hd16 showed a masking effect because of interactions with other heading date genes. Combinations of alleles at Hd1, Hd16, Hd17, and Hd18 resulted in approximately 20 days of variation in HD, and specific allele combinations exhibited 4-5 days earlier heading than ‘IS592BB,’ indicating their potential for developing early-harvest cultivars. QTLs for CL were detected on chromosomes 1 and 11, with SD1 (Semi-dwarf 1) and OsCPL3 (C-terminal domain phosphatase-like 3) identified as candidate genes. SD1 was associated with variations in the CL, PL, NS, and TGW. OsCPL3 was identified within QTL associated with CL and BRR, suggesting its potential involvement in variations in plant architecture and milling-related traits. Notably, the OsCPL3allele from ‘Koshihikari’ was associated with higher BRR compared to that from ‘IS592BB,’ indicating its potential utility as a favorable allele for improving milling quality in rice breeding programs.