Multifunctional nanoparticles have contributed to several advances in the biomedical field. For example, many have been shown to provide higher level analysis in fundamental studies on cancer and regenerative medicine. Application of multifunctional nanoparticles as contrast agents or probes for diagnostic imaging enables integration of various imaging modalities which provides greater detail and more accurate information for diagnosis. In addition, these multifunctional materials may help researchers and clinicians combine diagnostics and treatment, called theranostics or image-guided therapy, for minimally invasive treatment of metastatic and minute cancers. Based on the viewpoint of the toxicity and the easily-controlled surface characteristics, shape, and internal function of silica-based hybrid nanoparticles, this review describes that the hybrid nanoparticles break ground for various analytical methods for fundamental studies, diagnostic techniques, and therapies. In particular, the present review focuses on seamless imaging, dual-modal imaging, and image-guided therapy using silica-based multifunctional hybrid nanoparticles with visible and near-infrared fluorescence, as well as X-ray-absorbing, photoresponsive, drug-releasing, and photoinduced heat-and reactive oxygen species-generating capabilities.