Understanding the atomic structure and structural instability of organic-inorganic hybrid perovskites is the key to appreciate their remarkable photoelectric properties and understand failure mechanism. Here, using low-dose imaging technique by direct-detection electron-counting camera in a transmission electron microscope, we investigate the atomic structure and decomposition pathway of CH₃NH₃PbI₃ (MAPbI₃) at the atomic scale. We successfully image the atomic structure of perovskite in real space under ultra-low electron dose condition, and observe a two-step decomposition process, i.e., initial loss of MA⁺ followed by the collapse of perovskite structure into 6H-PbI₂ with their critical threshold doses also determined. Interestingly, an intermediate phase (MA_0.5PbI₃) with locally ordered vacancies can robustly exist before perovskite collapses, enlightening strategies for prevention and recovery of perovskite structure during the degradation. Associated with the structure evolution, the bandgap gradually increases from ~1.6 eV to ~2.1 eV. In addition, it is found that C-N bonds can be readily destroyed under irradiation, releasing NH₃ and HI and leaving hydrocarbons. These findings enhance our understanding of the photoelectric properties and failure mechanism of MAPbI₃, providing potential strategies into material optimization.