The recombinant inbred line population, which was derived from a hybridization of the japonica variety Asominori and the indica variety IR24, was deployed for the quantitative trait locus (QTL) mapping for the genetic components underlying the heading date (HD) in two environments (Nanjing and Hainan, both from China). As a result, five and six QTLs were detected from both locations respectively. Of them, this locus qDTH-6 on chromosome 6 could be simultaneously detected with LOD values of 6.28 and 12.93, and with the contribution rates of 12.26 and 17.18, respectively. Moreover, this line CSSL45, which is one of IR24 chromosome segment substitution lines (CSSL) and which contains qDTH-6, and its background parental line were treated under short-day (SD) condition. The qDTH-6 allele from IR24 showed dominant photo-inhibition. By analyzing a set of heading date tester lines and some tester cultivars crossed with CSSL45, we speculated that the qDTH-6 allele from IR24, which names Su-E1(t), inhibited the function of photoperiod-sensitive gene E1 (Ghd7). Using CSSL45 × Asominori secondary F2 population, Su-E1(t) was further localized close to SSR marker RM527. Taken together, the results might be of significance in order to shorten the heading date of indica-japonica hybrid.