Gd-doped quantum dots (QDs) have been widely used as small-sized bifunctional contrast agents for fluorescence/magnetic resonance (FL/MR) dual-modality imaging. However, Gd doping will always compromise the FL of host QDs. Therefore, balancing the Gd doping and the optical properties of QDs is crucial for constructing high-performance bifunctional nanoprobes. Additionally, most paramagnetic QDs are synthesized in the organic phase and need to be transferred to the aqueous phase for bioimaging. Herein, ingeniously designed shell-doped Cu-In-S/ZnS:Gd QDs have been prepared in the aqueous phase. It has been demonstrated that isolating paramagnetic Gd from fluorescent Cu-In-S core via doping Gd into ZnS shell not only avoided the decrease of FL quantum yield (QY), but also ensured the water accessibility of paramagnetic Gd ions, by which the FL QY and r relaxivity of Cu-In-S/ZnS:Gd QDs achieved as much as 15.6% and 15.33 mM·s, respectively. These high-performance QDs with excellent stability, low biotoxicity, and good tumor permeability were successfully applied for in vivo tumor FL/MR dual-modality imaging, and have shown significant potential in the precision detection and diagnosis of diseases.