Phosphorene, a monolayer of black phosphorus (BP), is an elemental two-dimensional material with interesting physical properties, such as high charge carrier mobility and exotic anisotropic in-plane properties. To fundamentally understand these various physical properties, it is critically important to conduct an atomic-scale structural investigation of phosphorene, particularly regarding various defects and preferred edge configurations. However, it has been challenging to investigate mono- and few-layer phosphorene because of technical difficulties arising in the preparation of a high-quality sample and damages induced during the characterization process. Here, we successfully fabricate high-quality monolayer phosphorene using a controlled thinning process with transmission electron microscopy and subsequently perform atomic-resolution imaging. Graphene protection suppresses the e-beam-induced damage to multilayer BP and one-side graphene protection facilitates the layer-by-layer thinning of the samples, rendering high-quality monolayer and bilayer regions. We also observe the formation of atomic-scale crystalline edges predominantly aligned along the zigzag and (101) terminations, which is originated from edge kinetics under e-beam-induced sputtering process. Our study demonstrates a new method to image and precisely manipulate the thickness and edge configurations of air-sensitive two-dimensional materials.