The solvothermal synthesis of CdTe nanocrystals in dimethylformamide using cadmium lactate and sodium hydrogen telluride as precursors and 1-thioglycerol as a stabilizer is described. The resultant nanocrystals can be dispersed in the mixture solution of ammonium hydroxide, water, ethanol, and tetraethyl orthosilicate without aggregation and therefore readily encapsulated in silica submicrospheres without ligand exchange through the Stöber process. CdTe nanocrystals of up to three different emission colors are encapsulated in silica spheres at varying emission intensity ratios, allowing for both wavelength and intensity encoding. A two-step growth process is also employed for the preparation of core-shell silica spheres, with differently sized CdTe nanocrystals encapsulated separately in the core and shell regions. Solid core-mesostructured shell silica spheres are further prepared. The mesostructured shell functions as a matrix for both nanocrystals and organic fluorophores. Our preparation approach is highly versatile and efficient. It offers potentials for the creation of optically encoded silica submicrospheres for many optical and biotechnological applications.