The abnormal change of lipid droplets (LDs) polarity has been believed to be closely associated with many diseases such as fatty liver. Thus, the detection of LDs polarity plays a particular role in the diagnosis of LDs polarity-related diseases. Herein, two isoindole-based fluorescent probes have been derived and they show evident solvatochromic effects, large two-photon absorption cross-section, LDs-specificity, and high photostability and excellent performance in monitoring LDs-polarity changes in living cells. Owing to the existence of intramolecular charge transfer process, these isoindole-based probes exhibited high sensitivity between the emission wavelength maxima and solvent polarity. In spite of that, they maintained high fluorescence quantum yields up to 0.87. Moreover, the detection of LDs-polarity was demonstrated in living cells via confocal laser scanning fluorescence imaging. Importantly, the isoindole-based probe maintained strong fluorescence with high contrast and clarity after seven days of degradation in a zebrafish model, indicating that it is photostable enough and suitable for long-term tracking and observation of biological dynamic changes. All these features render the isoindole chromophore an effective implement for the diagnosis of LDs polarity-related diseases.