A population of 120 double-haploid lines derived from Samgang/Nagdong was used for analyzing the developmental behaviors of plant height and tiller number by conditional mapping via composite interval approaches at five growth stages of rice. The traits were normally distributed with transgressive segregations in both directions. A total of 4 QTLs associated with plant height were identified in 40th/initial, 50th/40th and 60th/50th periods, respectively. The qph7.1 was observed in 50th/40th and 60th/50th periods, with increasing effects from Samgang and Nagdong alleles, respectively. This indicated that an individual gene or genes at the same genomic region might have opposite genetic effects at various growth stages. Five QTLs associated with tiller number were identified in four stages except 60th/50th stage. Four of five increasing effects of QTLs were from Nagdong alleles. Six of nine QTLs for two traits were detected before 60 days. It was evident that the expression of QTLs for plant height and tiller number was more active at early stages than at maturity stage. Furthermore, QTLs identified at early stages showed opposite additive effects on plant height and tiller number. These results provided a possible genetic explanation for the negative correlation between two traits.