Point and line defects are of vital importance to the physical and chemical properties of certain two-dimensional (2D) materials. Although electron beams have been demonstrated to be capable of creating single- and multi-atom defects in 2D materials, the products are often random and difficult to predict without theoretical inputs. In this study, the thermal motion of atoms and electron incident angle were additionally considered to study the vacancy evolution in a black phosphorus (BP) monolayer by using an improved first-principles molecular dynamics method. The P atoms in monolayer BP tend to be struck away one by one under an electron beam within the displacement threshold energy range of 8.55–8.79 eV, which ultimately induces the formation of a zigzag-like chain vacancy. The chain vacancy is a thermodynamically metastable state and is difficult to obtain by conventional synthesis methods because the vacancy formation energy of 0.79 eV/edge atom is higher than the typical energy in monolayer BP. Covalent-like quasi-bonds and a charge density wave are formed along the chain vacancy, exhibiting rich electronic properties. This work proposes a theoretical protocol for simulating a complete elastic collision process of electron beams with 2D layers and will facilitate the establishment of detailed theoretical guidelines for experiments on 2D material etching using focused high-energy electron beams.