Transmission electron microscopy (TEM) offers unprecedent atomic resolution imaging and diverse characterizations capabilities, which has been proved to be effective in correlating the atomic structures and compositions with the physical/chemical properties of semiconductor nanomaterials. This review aims to provide an overview of the latest advancements regarding the atomic structure/property relationship in semiconductor nanomaterials. First, by employing off‐axis electron holography, a comprehensive overview of the quantitative investigations into the atomic‐electronic structure relationship of semiconductors is presented. Second, by integrating in situ TEM technique with micro/nanoelectromechanical systems (M/NEMS), this review summarizes the recent advancements achieved in elucidating the intricate relationship between structure and properties of nanomaterials subjected to diverse stimuli such as stress, thermal, and electric fields. Moreover, the impact of electron beam irradiation on the microstructure of semiconductor nanomaterials is discussed. Lastly, current challenges and future research opportunities are proposed along with their potential applications.