A series of hydroxy thiophene-conjugated benzothiazole derivatives (HTBs) was prepared to investigate their fluorescence emission behaviors and capability to selectively stain subcellular organelles for fluorescence imaging. The HTB derivatives exhibited excited-state intramolecular proton transfer (ESIPT) and intramolecular charge transfer (ICT) behaviors, according to their molecular structure. Subtle changes in the molecular structure of the HTB influenced its response to changes in the surrounding environment, such as the solvent polarity and/or pH. In vitro cellular imaging experiments revealed that HTBA (5-(benzo[d]thiazol-2-yl)-[2,2′-bithiophen]-4-ol) could selectively stain mitochondria. In contrast, HTBB-CO2Et (ethyl 5'-(benzo[d]thiazol-2-yl)-3′-hydroxy-[2,2′-bithiophene]-5-carboxylate), which contains a regioisomeric hydroxy thiophene unit with an electron-withdrawing ethyl ester group, showed the capability to stain lipid droplets (LDs) in living cells. When the hydroxyl group in HTBB-CO2Et was protected with a benzyl group, effective staining of LDs in live cells was achieved. Thus, we successfully obtained an effective fluorescent probe. Collectively, the results indicated that small structural changes resulted in substantial changes in the intracellular localization and in vitro imaging ability of the prepared compounds.