As a crucial constituent of the endomembrane system in eukaryotic cells, the Golgi apparatus serves as a major transport hub for intracellular macromolecular transport. Its dysfunction is closely related to various diseases including malignancy and neurodegenerative diseases. In order to comprehend the pathological role of Golgi apparatus and its associated signaling molecules in diseases, a variety of assays for the measurement of Golgi biomarkers have been developed. Among them, small molecule fluorescent probes play an irreplaceable role in real-time in situ imaging of biomarkers due to their unique advantages such as high sensitivity, high spatial and temporal resolution, excellent reproducibility and low toxicity. In recent times, there has been a significant focus on the utilization of Golgi-targeted fluorescence probes to identify Golgi-related biomarkers in various human diseases. This review aims to comprehensively outline the recent advancements in Golgi-targeted small-molecule fluorescent probes, with emphasis on their chemical structures, detection mechanisms and applications. In addition, we present existing challenges in Golgi imaging and suggestions for the development of novel Golgi-targeted small-molecule fluorescence probes to facilitate research on Golgi-related diseases and signaling pathways.