Abstract: Abstract：[Objective] The objective of our study was to investigate the characters of root traits and the genetic mechanism of rice drought tolerance, explore the favorable genes of upland rice, and provides a theoretical basis and research materials in cultivating high-yield and drought-resistance species from the hybrid generations of upland and lowland rice. [Method]A set of 180 introgression lines (ILs) population between an accession of upland rice Haogelao, as donor, and lowland rice Shennong265, as the recipient, was developed using 187 SSR markers. The QTLs at heading stage for six root traits namely MRL (maximum root length), TRN (thick root number), TNR (total numbers of root), ART (average root thickness), RDW (root dry weight) and TPW (total plant mass weight) were mapped using single-marker regression analysis. [Result]A total of 38 putative QTLs for six root traits were detected using single marker analysis at heading stage. 6 QTLs associated with MRL were detected and the total contribution rate was 29%. A total of 6 QTLs affected to TRN were found at jointing stage and explained 27% phenotypic variance. 4 QTLs about TNR were detected and the total contribution rate was 21%. 6 QTLs which controlled the ART were detected and can explain 33% phenotypic variance. 4 QTLs related to RDW were identified in this study and the total contribution rate was 23%. 12 QTLs associated with TPW were detected and which could explain 61% of the phenotypic variance. 3 and 1 QTLs derived from Haogelao caused a decrease effect of TRN and TNR respectively. The additive effects of the characters were relatively large except ART. [Conclusion] 89.5% QTLs derived from upland rice Haogelao improved the six root traits of the ILs in genetic background of lowland rice Shennong265. QTLs about different root traits distributed most in clusters on chromosome. Four QTLs were detected near RM3853. So, we speculated that RM3853 must be a new gene cluster related to root traits and drought tolerance of rice at heading stage.