Quantum dots (QDs), as one of the emerging nanomaterials, have been widely studied by scientists due to their advantages and potential in bioimaging, especially cell imaging. Cadmium (Cd)‐based QDs, which have the best photoluminescence property, have received widespread attention. However, due to the obvious toxicity problem of these QDs, their cell imaging application is hindered. Recently, the emergence of Cd‐free‐metal and metal‐free QDs with lower toxicity makes people consider that Cd‐based QDs may be substituted by these QDs. However, problems of these QDs in cytotoxicity also cannot be ignored. Some reports claimed that their prepared emerging QDs for cell imaging were low toxicity, but there still exist up‐regulation of oxidative stress, inflammation, and apoptosis from other reports. And, up to now, few reports have separately summarized and discussed the issues of cell imaging and cytotoxicity of different types of QDs. Therefore, in this review, we classify QDs as following three types, Cd‐based, Cd‐free‐metal and metal‐free QDs, focus on the cell, the essential unit of life, discuss cell imaging application and cytotoxicity of QDs, and finally elucidate main mechanisms of cytotoxicity respectively. This review provides reference for the toxicity evaluation of QDs and highlights the potential cytotoxicity of Cd‐free QDs.