A novel strategy of preparing multifunctional nanoparticles (NPs) with near infra red (NIR) fluorescence and magnetism showing good hydrophilicity and low toxicity was developed via surface-initiated atom transfer radical polymerization with activators generated by electron transfer (AGET ATRP) of poly(ethylene glycol) monomethyl ether methacrylate (PEGMA) and glycidyl methacrylate (GMA) employing biocompatible iron as the catalyst on the surface of silica coated iron oxide (Fe3O4@SiO2) NPs. The small molecules (CS2), a NIR fluorescent chromophore, can be fixed into the covalently grafted polymer shell of the NPs by chemical reaction through a covalent bond to obtain stable CS2 dotted NPs Fe3O4@SiO2@PPEGMA-co-PGMA@CS2. The fluorescence intensity of the as-prepared NPs could be conveniently regulated by altering the silica shell thickness (varying the feed of silica source TEOS), CS2 feed, or the feed ratio of VPEGMA/VGMA, which are easily realized in the preparation process. Thorough investigation of the properties of the final NPs including in vivo dual modal imaging indicate that such NPs are one of the competitive candidates as imaging agents proving a promising potential in the biomedical area.