In recent years, aggregation-induced emission enhancement (AIEE) molecules have shown great potential for applications in the fields of bio-detection, imaging, optoelectronic devices, and chemical sensing. Based on our previous studies, we investigated the fluorescence properties of six flavonoids and confirmed that compounds1–3have good aggregation-induced emission enhancement (AIEE) properties through a series of spectroscopic experiments. Compounds with AIEE properties have addressed the limitation imposed by the aggregation-caused quenching (ACQ) of classic organic dyes owing to their strong fluorescence emission and high quantum yield. Based on their excellent fluorescence properties, we evaluated their performance in the cell and we found that they could label mitochondria specifically by comparing their Pearson correlation coefficients (R) with Mito Tracker Red and Lyso-Tracker Red. This suggests their future application in mitochondrial imaging. Furthermore, studies of uptake and distribution characterization in 48 hpf zebrafish larvae revealed their potential for monitoring real-time drug behavior. The uptake of compounds by larvae varies significantly across different time cycles (between uptake and utilization in the tissue). This observation has important implications for the development of visualization techniques for pharmacokinetic processes and can enable real-time feedback. More interestingly, according to the data presented, tested compounds aggregated in the liver and intestine of 168 hpf larvae. This finding suggests that they could potentially be used for monitoring and diagnosing liver and intestinal diseases.