The heading date is an important trait that determines the yield and quality of rice, and plays an important role in the process of rice breeding, seed production, introduction and domestication. In this study, F1 was obtained by a cross between Nekken2 (Oryza sativa subsp. japonica cv. ‘Nekken2’) and Huazhan (O. sativa subsp. indica cv. ‘HZ’), and 120 recombination inbred lines (RILs) were obtained through successive multi-generational selfing. The population of RILs was used as experimental material. Under the condition of conventional water and fertilizer management, the time of heading stage of 120 lines was analyzed. Using the high-density genetic map constructed by this population, the QTLs for the heading date was mapped and analyzed. A total of 11 QTLs were detected on chromosomes 1, 3, 4, 5, 6, 8, and 12, respectively, and one of the LOD values was as high as 5.75. By analyzing the candidate genes in the QTLs interval, the related genes that may affect the heading date were screened out, and real-time quantitative PCR was used for gene expression analysis. The expression levels of six genes, LOC_Os03g03070, LOC_Os03g50310, LOC_Os03g55389, LOC_Os04g55510, LOC_Os08g07740, and LOC_Os08g01670 significantly different between parents, and the expression of LOC_Os03g50310 in Nekken2 was 3.6 times higher than that in HZ. In addition, the sequencing analysis showed that there were 4 differences in the 5'UTR, CDS region and 3'UTR of the candidate gene LOC_Os03g50310 between the parents, of which the single nucleotide polymorphisms (SNP) difference in the CDS region caused a single amino acid change. This study provides new clues for further cloning of heading date-related genes and cultivar selection by mining the QTL loci related to heading date in rice.