Halide perovskites are strategically important in the field of energy materials. Along with the rapid development of the materials and related devices, there is an urgent need to understand the structure–property relationship from nanoscale to atomic scale. Much effort has been made in the past few years to overcome the difficulty of imaging limited by electron dose, and to further extend the investigation towards operando conditions. This review is dedicated to recent studies of advanced transmission electron microscopy (TEM) characterizations for halide perovskites. The irradiation damage caused by the interaction of electron beams and perovskites under conventional imaging conditions are first summarized and discussed. Low-dose TEM is then discussed, including electron diffraction and emerging techniques for high-resolution TEM (HRTEM) imaging. Atomic-resolution imaging, defects identification and chemical mapping on halide perovskites are reviewed. Cryo-TEM for halide perovskites is discussed, since it can readily suppress irradiation damage and has been rapidly developed in the past few years. Finally, the applications of in-situ TEM in the degradation study of perovskites under environmental conditions such as heating, biasing, light illumination and humidity are reviewed. More applications of emerging TEM characterizations are foreseen in the coming future, unveiling the structural origin of halide perovskite’s unique properties and degradation mechanism under operando conditions, so to assist the design of a more efficient and robust energy material.