CdTe/CdS/ZnS core-shell-shell (CSS) quantum dots (QDs) were synthesized in aqueous solution via water-bathing combined hydrothermal method using L-cysteine (L-Cys) as a stabilizer. This method possesses both the advantages of water-bathing and hydrothermal methods, and thus can prepare CSS QDs with markedly reduced synthesis time than previously reported methods. The as-prepared QDs display a higher fluorescent intensity than bare CdTe or CdTe/CdS. After co-cultured with yeast at different growth phase, the as-prepared L-Cys capped CdTe/CdS/ZnS QDs showed much less toxicity than the other CdTe or CdTe/CdS QDs. Our results demonstrate that the CSS QD would have a promising potential in fields of bio-labeling and cell imaging.