Organic–inorganic halide perovskites are promising photovoltaic materials with excellent optoelectronic properties. However, the extreme structural instability hinders their wide application as well as the microstructure characterization using high energy beams such as transmission electron microscopy (TEM). Here, taking BA2FAPb2I7 and BA2MAPb2I7 as examples, we investigate their structural evolution resulting from high energy electron irradiation, moist air, and low temperature, respectively. The results show that the long organic chains are the first to be damaged under electron beam, which is mainly arising from their instability and weak bonding with the framework of [PbI6]4− octahedrons. Then the short organic cations and the framework of [PbI6]4− octahedrons collapses gradually. The final products are clusters of detached PbI2 particles, which can also be observed in the sample degraded in moist air. In addition, the structures of BA2FAPb2I7 and BA2MAPb2I7 are discovered to undergo a phase transformation at liquid nitrogen temperature, which calls attention to the community that cryo-TEM methods should be used cautiously for organic–inorganic halide perovskite materials.