Super-resolution microscopy techniques are versatile and powerful tools for visualizing organelle structures, interactions, and protein functions in biomedical research, and its resolution ability to break the optical diffraction limit provides new analytical frameworks for cell biology on the nanoscale, which is indispensable to life science related fields. However, due to the effect of the diffraction limit, the axial resolution of a super-resolution microscope is more arduous to improve than the lateral resolution, which hinders the realization of sub-hundred-nanometer resolution three-dimensional imaging of cellular structures. Therefore, based on the two main techniques, stimulated emission depletion microscopy and single-molecule localization microscopy, the present paper introduces the principles and characteristics of a variety of existing three-dimensional imaging techniques, and finally discusses the future of that. Finally, we briefly discuss the research trend of the two techniques in the three-dimensional imaging area.