Covalent surface modification of silica nanoparticles (SNPs) offers great potential for the development of multimodal nanomaterials for biomedical applications. Herein, we report the synthesis of covalently conjugated bifunctional SNPs and their application to in vivo multimodal imaging. Bis(methallyl)silane 15 with cyclopropene and maleimide, designed as a stable bifunctional linker, was efficiently synthesized by traceless Staudiger ligation, and subsequently introduced onto the surface of monodispersed SNPs via Sc(OTf)3-catalyzed siloxane formation. The bifunctional linker-grafted SNP 20 underwent both thiol-conjugated addition and tetrazine cycloaddition in one pot. Finally, positron emission tomography/computed tomography and fluorescence imaging study of dual functional SNP [125I]28 labeled with NIR dye and 125I isotope showed a prolonged circulation in mice, which is conducive to the systemic delivery of therapeutics.