Nobiletin is a natural product with multiple physiological activities and is the main ingredient ofPericarpium Citri Reticulatae. We successfully discovered that nobiletin exhibits aggregation induced emission enhancement (AIEE) properties and it has significant advantages such as a large Stokes shift, good stability and excellent biocompatibility. The increase in methoxy groups endows nobiletin a greater fat-solubility, bioavailability and transport rate than the corresponding unmethoxylated flavones. Ulteriorly, cells and zebrafish were used to explore the application of nobiletin in biological imaging. It emits fluorescence in cells and is specifically targeted at mitochondria. Moreover, it has a noteworthy affinity for the digestive system and liver of zebrafish. Due to the unique AIEE phenomenon and stable optical properties of nobiletin, it paves the way for discovering, modifying and synthesizing more molecules with AIEE characteristics. Furthermore, it has a great prospect with regard to imaging cells and cellular substructures, such as mitochondria, which play crucial roles in cell metabolism and death. Indeed, three-dimensional real-time imaging in zebrafish provides a dynamic and visual tool for studying the absorption, distribution, metabolism and excretion of drugs. In this article, more directions and inspiration can be presented for the exploration of non-invasive pharmacokinetic research and intuitive drug pathways or mechanisms.