Luminescence nanoprobes have been extensively investigated for many biomedical applications, ranging from cell/tissue imaging, real‐time monitoring pathophysiological changes, drug discovery, bioassays, image‐guided surgery, and therapeutic evaluations, mainly due to their excellent physicochemical properties such as tailorable size, controlled morphology, and regulatable luminescence performances. In particular, rationally designed luminescence nanoprobes with reasonable functional integration enable pharmacological effect‐based drug screening, quantification of biological/pharmaceutical agents, and monitoring therapeutic responses of different drugs. This review provides an overview of the applications of different types of luminescence nanoprobes in drug discovery and development, involving various nanoprobes for high‐throughput and high‐content drug screening, pharmaceutical analysis, and therapeutic evaluations in cancers, cardiovascular diseases, and other typical inflammatory diseases. Moreover, challenges and future perspectives regarding future applications of luminescence nanoprobes in the drug discovery field are also discussed.