This work developed a multimodal imaging system by co-encapsulating superparamagnetic iron oxides (IOs) and quantum dots (QDs) in the nanoparticles of poly (lactic acid) - d-α-tocopheryl polyethylene glycol 1000 succinate (PLA-TPGS) for concurrent imaging of the magnetic resonance imaging (MRI) and the fluorescence imaging to combine their advantages and to overcome their disadvantages as well as to promote a sustained and controlled imaging with passive targeting effects to the diseased cells. The QDs and IOs-loaded PLA-TPGS NPs were prepared by a modified nanoprecipitation method, which were then characterized for their size and size distribution, zeta potential and the imaging agent encapsulation efficiency. The transmission electron microscopy (TEM) images showed direct evidence for the well-dispersed distribution of the QDs and IOs within the PLA-TPGS NPs. The cellular uptake and the cytotoxicity of the PLA-TPGS NPs formulation of QDs and IOs were investigated in vitro with MCF-7 breast cancer cells, which were conducted in close comparison with the free QDs and IOs at the same agent dose. The Xenograft model was also conducted for biodistribution of the QDs and IOs-loaded PLA-TPGS NPs among the various organs, which showed greatly enhanced tumor imaging due to the passively targeting effects of the NPs to the tumor. Images of tumors were acquired in vivo by a 7T MRI scanner. Further ex vivo images of the tumors were obtained by confocal laser scanning microscopy. Such a multimodal imaging system shows great advantages of both contrast agents making the resultant probe highly sensitive with good depth penetration, which confirms the diagnosis obtained from each individual imaging. With therapeutics co-encapsulation and ligand conjugation, such nanoparticles system can realize a multi-functional system for medical diagnosis and treatment.