Quantum dots (QDs), due to their superior luminous properties, have been proven to be a very promising biological probe, which can be used as a candidate material for clinical applications. The toxicity of QDs in the environment and biological systems has caused widespread concern in the nanosphere, but their immune toxicity and their impact on the immune system are still relatively unknown. At present, the research on the toxicity of QDs is mainly focused on in vitro models, but few have systematically evaluated their adverse effects on target organs. Animal studies have shown that QDs can be accumulated in various organs due to their main exposure routes, thereby posing a potential threat to major organs. This review briefly describes general characteristics and the wide medical applications of QDs and focuses on the adverse effects of QDs on major target organs, such as liver, lung, kidney, brain, and spleen, after acute and chronic exposure. QDs mainly cause changes in the corresponding indicators of target organs, such as oxidative damage, and in severe cases cause hyperemia, tissue necrosis, and even death. In addition to causing direct damage to target organs, QDs can also cause a large number of immune cells to accumulate and cause inflammatory reactions when causing damage to other major organs. Whether it is to avoid the risk of people contacting QDs in production and life, or to realize the clinical applications of QDs, is very essential to conduct systematic in vivo toxicity assessment of QDs.