Abstract: A recombinant inbred lines(RIL)population derived from a cross of XQZB/R9308 of a super hybrid rice Xieyou9308 was used to detect the quantitative trait loci(QTLs)for N-deficiency tolerance at different seedling stages by using cultural experiment. A total of 14 QTLs were detected, the detected QTL individually accounted for 7.13%-13.03% of the phenotypic variation, among the QTLs, six QTLs on chromosomes 1,7,1,7,10 and 11, respectively were detected on 15 days after treatment, and eight QTLs on chromosomes 3,8,3,10,3,8,10 and 4, respectively were detected on 30 days after treatment. One QTL within the interval RM297-RM212 on chromosome 1 was detected for relative shoot dry weight and relative total dry weight, which was associated with N recycling in rice. This chromosome region may be enriched with the key N metabolism genes. The results showed that the QTL of differential expression of the two periods of N-deficiency tolerance were closely related to the genes of temporal and spatial expression of different developmental stages in rice, which reflected on the site differences of N-deficiency tolerance.