Scanning/transmission electron microscopy (STEM) is a powerful characterization tool for a wide range of materials. Over the years, STEMs have been extensively used for in situ studies of structural evolution and dynamic processes. A limited number of STEM instruments are equipped with a secondary electron (SE) detector in addition to the conventional transmitted electron detectors, i.e., the bright field (BF) and annular dark field (ADF) detectors. Such instruments are capable of simultaneous BF-STEM, ADF-STEM, and SE-STEM imaging. These methods can reveal the “bulk” information from BF and ADF signals and the surface information from SE signals for materials less than 200 nm thick. This review first summarizes the field of in situ STEM research, followed by the generation of SE signals, SE-STEM instrumentation, and applications of SE-STEM analysis. Combining with various MEMS-based in situ heating, gas reaction, and mechanical testing stages, we show that simultaneous SE-STEM imaging has found applications in studying the dynamics and transient phenomena of surface reconstructions, exsolution of catalysts, lunar and planetary materials, and mechanical properties of 2D thin films. Finally, we provide an outlook on the potential advancements in SE-STEM from the perspective of sample-related factors, instrument-related factors, and data acquisition and processing.