Observing dynamic interaction between organelles and analyzing the law of action is of great significance for revealing the mechanism behind the phenomenon of physiological and pathological processes. Due to the limitation of the optical diffraction determined by wavelength and aperture, traditional optical microscopes cannot observe the nanoscale fine structure of organelles and the dynamic changes of interactions among them. The emergence of super-resolution microscopy imaging technology provides an important mean for the study of organelle interaction. This paper introduces the fluorescence microscopy (STED), structured illumination imaging (SIM), and single-molecule localization imaging (SMLM). The application of these super-resolution microscopy in the study of dynamic interaction between organelles provides the expansion of application ideas for super-resolution microscopy. Finally, the advantages and disadvantages of super-resolution microscopy in the study of organelle interactions are analyzed. In conclusion, the demand and development trend of super-resolution microscopy technology in the imaging of intracellular organelle interaction in living cells is prospected, which provides a certain reference for the cross-integration development of optics, medicine and biology.