We compared the effects of several ligands frequently used in aqueous synthesis, including L-cysteine, L-cysteine hydrochloride, N-acetyl-L-cysteine (NAC), glutathione and 3-mercaptopropionic acid, for microwave synthesis of CdTe quantum dots (QDs) in a sealed vessel with varied temperatures and times, and then developed a rapid microwave-assisted protocol for preparing highly luminescent, photostable and biocompatible CdTe/CdS/ZnS core-multishell QDs. The effects of molecular structures of these ligands on QD synthesis under high temperatures were explored. Among these ligands, NAC was found to be the optimal ligand in terms of the optical properties of resultant QDs and reaction conditions. The emission wavelength of NAC-capped CdTe QDs could reach 700 nm in 5 min by controlling the reaction temperature, and the resultant CdTe/CdS/ZnS core-multishell QDs could achieve the highest quantum yields up to 74% with robust photostability. In addition, the effects of temperature, growth time and shell-precursor ratio on shell growth were examined. Finally, cell culturing indicated the low cytotoxicity of CdTe/CdS/ZnS core-multishell QDs as compared to CdTe and CdTe/CdS QDs, suggesting their high potential for applications in biomedical imaging and diagnostics.