In this study, only two of 12 quantitative trait loci (QTLs) affecting yield and yield components were identified in a single year, indicating that individual QTLs are probably sensitive to the environment. A rice growth survey of “Cheongcheong” and “Nag dong” in a doubled haploid population in 2012 revealed that yield capacity was influenced by climate change. Analysis of yield and yield components indicated that five average traits are high in “Cheongcheong”. Frequency distribution tables indicated that panicles per plant (PPP), spike lets per panicle (SPP), and 1000-grain weight (TGW) were normally distributed. The strongest relationship was identified between SPP and seed set percentage (SSP) among phenotypic correlations related to yield and yield components found on chromosomes 2, 3, 6, 8 in 2012. SPP and SSP was a very relevant requisite about quantity. Analysis of QTL about quantity was total 9. In the present study, a doubled haploid population was used to analyze the epistatic effects on yield and yield components in rice. Although other epistatic QTLs were not included in any of the main-effect QTLs, they significantly influenced the traits. These results indicated that epistatic interaction plays an important role in controlling the expression of complex traits. Thus, the utilization of marker-assisted selection in rice breeding programs should take epistatic effects into consideration. Hence, the QTLs responsible for major effects are more suitable for marker-assisted selection programs to improve yield and related traits across different environments.