Technological progress has played an irreplaceable role in the establishment and development of cell biology. Without the invention of the microscope, there would be no cell theory. Similarly, the achievements in cell biology to date would not have been possible without the development of electron microscopy (EM) and its integration with molecular biology. The application of many new techniques and methodological breakthroughs have directly led to important advances and the formation of new concepts in cell biology. Although EM can image biological samples at the near‐nanometer resolution, morphological changes resulting from sample processing remain a major concern. The development of scanning probe microscopy (SPM) has further extended perceptions of the cellular world to the nanometer level of resolution. Among SPM techniques, atomic force microscopy (AFM) helps to overcome the limitations of optical and EM, making it possible to determine the three‐dimensional (3D) structure of cell membranes. The advantages of AFM – such as simple sample preparation, no special treatment, and the near‐physiological conditions of the imaging environment – can maintain the original shape of biological samples. The unique ability of AFM to determine the 3D structure and function of cell membranes provides a new perspective for understanding the entire character of cell membranes at a nanoscale to a sub‐nanoscale resolution and in realtime, which has contributed to the birth of the field of biomembranomics. This article will discuss the use of AFM for the imaging analysis of cell membrane structure and function, the combination of AFM with super‐resolution techniques, and the progress made in these analytical methods.