The core restorer line is a kind of restorer lines which has been widely used in hybrid rice breeding practice. The study on the genetic basis of core restorer lines and identification of QTL/gene underlying important agronomic traits will facilitate the restorer development by the molecular marker assisted selection in rice. In this study, the population with 250 recombinant inbred lines (RIL) was developed with a three-line core restorer Chenghui727 and a two-line restorer 9311 as parents, both have been widely used in hybrid rice breeding. The evaluation of 9 important agronomic traits and genotypic analysis of SSR markers were conducted in Sanya, Hainan of 2015 and Hefei, Anhui of 2016. The phenotype data was analyzed with SAS9.2. QTLs were mapped and analyzed by QTL IciMapping v4.1 software. A total of 39 QTLs were detected in two environments, among which 16 QTLs were identified in Sanya and located on the chromosome 1,2,4,7,8,10,11 and 12, 24 QTLs were identified in Hefei and located on the chromosome 1,2,3,7,8,9,10 and 12. The qPH1-1 was detected in both Sanya and Hefei, of which the additive effects are -1.75 and -2.46 respectively. The increasing alleles of 13 QTLs come from Chenghui727 and 16 QTLs from 9311. There are 26 QTLs identified here had been reported by the previous study and 13 QTLs are newly detected in this study. In addition, 5 pleiotropic QTLs were found in the intervals of RM279—RM521, RM336—RM3534, RM25—RM547, RM553—RM160 and RM222—RM271. Among which the interval of RM25—RM547 was near the cloned gene Ghd8. The QTL located in RM553—RM160 was a novel pleiotropic QTL underlying the filled grain number per plant, grain yield per plant and spikelet fertility with large addivite effects and contributed more than 5% of the phenotypic variation. The other three pheiotropic QTLs had been reported in previous study as a single QTL, however the pleiotropism was found in this study only. In present study, all the newly found QTL e.g. qPN12-1 underlying panicle number, QTL qPL1-2 and qPL10-1 underlying panicle length, QTL qSNP2-1 and qSNP10-1 underlying spikelet number per panicle, qSF3-1 underlying spikelet fertility rate, QTL qTGW7-1 underlying grain weight and qGY1-1 underlying grain yield have large additive effects and explained high proportion of phenotypic variation. The results in this study will be helpful to the fine mapping, cloning and breeding for the related traits.