Quantitative trait loci (QTL) analysis on abortion of apical spikelet was conducted by using recombinant inbred lines (RILs) derived from a cross between indica variety Guichao 2 and Koshihikari under three environments. The abortion trait of apical spikelets in the recombinant inbred lines demonstrated a continuous distribution together with transgressive segregations. Six QTLs were mapped on the chromosomes 1,2,3,5,6 and 7 in RIL populations, explaining 4.49% -9.74% phenotypic variations. Among these QTLs, qASA2 was detected at the interval flanked by the markers RM3355 and RM263 on chromosome 2 under different environments. qASA1 was mapped between the markers RM6451 and OSR13 on chromosome 1 with its positive alleles from Guichao 2.