Multifunctional nanoparticles (NPs) have great potential for multimodal cancer imaging and effective therapy. We have developed multifunctional NPs (GNR@SiO2@QDs) by incorporating gold nanorods (GNRs) and CdSe/ZnS quantum dots (QDs) into silica. Folic acid (FA) as a targeting ligand was covalently conjugated on the surfaces of GNR@SiO2@QDs with a silane coupling agent. Cell viability assay showed that these NPs had low cytotoxicity. And confocal fluorescence images illustrated that they could selectively target HeLa cells overexpressing folate receptors (FRs) rather than FR-deficient A549 cells. In vitro cell imaging experiments revealed that these NPs exhibited strong X-ray attenuation for X-ray computed tomography (CT) imaging and strong fluorescence for fluorescence imaging. They also showed an enhanced photothermal therapy (PTT) effect for cancer cells due to GNRs' high absorption coefficient in the near infrared (NIR) region and a better heat generation rate. All results show that they have great potential in theranostic applications such as for targeted tumor imaging and therapy.