Highly fluorescent SiO2@CdTe@SiO2 (SQS) nanoparticles as a new nanoprobe in biomedical imaging have been successfully synthesized by a novel approach. The size of SQS can be tuned from 39 to 76 nm by controlling reaction parameters, including the amount and the type of silica precursor, the ratio of silica precursor to ammonia solution, and the ratio of H2O to surfactant. The photo- and chemical stability, cytotoxicity and cell uptake of these nanoparticles were investigated. The results demonstrate that these properties are strong size-dependent, and reveal that the minimal shell thickness for effective protection of the embedded CdTe quantum dots is 6 nm. Our findings highlight the importance of controlling particle size and shell thickness during the preparation of fluorescent silica-QDs core-shell nanoparticles, and their potential in cell labeling and imaging.