A general polyelectrolyte-mediated self-assembly technique is adopted to prepare multifunctional mesoporous nanostructures as an effective biological bimodal imaging probe and magnetically targeted anticancer drug (doxorubicin) delivery systems (DDSs). A positively charged polyelectrolyte (PAH) and negatively charged fluorescent quantum dots (QDs) are successfully assembled onto the surface of ellipsoidal Fe3O4@SiO2@mSiO2 composite nanostructures to combine the merits of tunable fluorescent/magnetic properties, mesoporous nanostructures for drug loading, and the uniform ellipsoidal morphology for enhanced uptake by cancer cells. The resultant nanoellipsoids are homogeneously coated with four layers of PAH/QDs, with an additional PAH layer to make the ellipsoidal surface positively charged. This acts to enhance cellular uptake, which is driven by electrostatic interactions between the positive nanoparticle surface and the negative cell surface. The high biocompatibility of the achieved multifunctional nanoellipsoids is demonstrated by a cell-cytotoxicity assay, hemolyticity against human red blood cells, and coagulation evaluation of fresh human blood plasma after exposure to the nanoparticles. Moreover, confocal microscopy and bio-TEM observations show that the cell uptake of nanocarriers is dose-dependent, and the nanoparticles accumulate mostly in the cytoplasm. The excellent capability of the nanocarriers as contrast agents for MRI is demonstrated by the relatively high r2 value (143 mM−1s−1) and preliminary in vivo characterization. More importantly, the doxorubicin-loaded DDSs show higher cytotoxicity than the free doxorubicin drug as contributed by the intracellular release pathway of doxorubicin from the DDSs, indicating the potential application of the obtained multifunctional mesoporous nanoellipsoids as highly effective bimodal imaging probes and DDSs for cancer diagnosis and chemotherapy, simultaneously.