Farmland soil is gradually polluted by cadmium (Cd), which leads to the excessive Cd concentration in grain. Food security has attracted much attention of people all over the world. Therefore, the utilization of Cd polluted farmland soil and reduction of the Cd concentration in grain have become an urgent issue to be resolved. Yahui2816, a low grain Cd-accumulating rice line with high shoot Cd-accumulation, is potential to achieve these goals simultaneously. The genetic stability of shoot Cd accumulation and the relevant genetic basis in Yahui 2816 was investigated in this study, providing an idea for molecular marker-assisted selection of low grain Cd-accumulating rice with high shoot Cd accumulation. Three types of F₁ hybrids were constructed by rice restorer line Yahui 2816 and three male sterile lines (Lu98A, 5406A and C268A) to analyze the heterosis of shoot Cd accumulation. The F₂ population was constructed by Yahui2816 and C268A. The F₁ population (constructed by Yahui2816 and C268A) showed a distinct advantage and thus met the basic requirement of quantitative trait locus (QTL) analysis of phenotypic isolation. Furthermore, the F₂ was used to analyze the QTLs of shoot Cd accumulation combined with the genetic linkage map. The results revealed that:(1) F₁ hybrids showed a good heterosis phenomenon of shoot Cd accumulation, indicating Yahui2816 had strong genetic stability. Meanwhile, a mid-/super-parent segregation was observed in F₂ population. (2) A QTL controlling shoot biomass (qSB-6) and three QTLs controlling shoot Cd accumulation (qSCdA-4, qSCdA-6-1 and qSCdA-6-2) were detected on chromosome 4 and 6, explaining 10.6%-14.4% of the phenotypic variance in the shoot Cd accumulation of the F₂ population. (3) Shoot Cd accumulation showed significantly positive correlations with shoot biomass and Cd concentration, root and grain biomass and Cd accumulation, transfer factor of Cd to shoot, and a negative correlation with transfer factor of Cd to grain. In addition, there were 4 overlap regions (Cl-4-1, Cl-6-1, Cl-6-2 and Cl-6-3) controlling two or more traits at the same time. (4) Marker 04171-marker 04197 controlled shoot biomass and Cd accumulation simultaneously and did not overlap with the QTLs controlling grain Cd concentration. In conclusion, Yahui2816 carried an allele which can enhance the ability of shoot Cd accumulation, and its related traits could be stably inherited from generation to generation. QTLs (qSCdA-4, qSCdA-6-1 and qSCdA-6-2) controlling shoot Cd accumulation were beneficial for molecular marker-assisted breeding of rice with high shoot Cd accumulation and low grain Cd accumulation.