The need for novel design strategies for fluorescent nanomaterials to improve our understanding of biological activities at the molecular level is increasing rapidly. Dye-doped fluorescent silica nanoparticles (SiNPs) emerge with great potential for developing fluorescence imaging techniques as a novel and ideal platform for the monitoring of living cells and the whole body. Organic dye-containing fluorescent SiNPs exhibit many advantages: they have excellent biocompatibility, are non-toxic, highly hydrophilic, optically transparent, size-tunable and easily modified with various biomolecules. The outer silica shell matrix protects fluorophores from outside chemical reaction factors and provides a hydrophilic shell for the insoluble nanoparticles, which enhances the photo-stability and biocompatibility of the organic fluorescent dyes. Here, we give a summary of the synthesis, characteristics and applications of fluorescent SiNPs for non-invasive fluorescence bioimaging in live cells and in vivo. Additionally, the challenges and perspectives of SiNPs are also discussed. We prospect that the further development of these nanoparticles will lead to an exciting breakthrough in the understanding of biological processes.