Two-dimensional (2D) materials containing hole defects are a promising substitute for conventional nanopore membranes like silicon nitride. Hole defects on 2D materials, as atomically thin nanopores, have been used in nanopore devices, such as DNA sensor, gas sensor and purifier at lab-scale. For practical applications of 2D materials to nanopore devices, researches on characteristics of hole defects on graphene, hexagonal boron nitride (hBN) and molybdenum disulfide (MoS2) have been conducted precisely using transmission electron microscopy (TEM). Here, we summarized formation, features, structural preference and stability of hole defects on 2D materials with atomic-resolution TEM images and theoretical calculations, emphasizing the future challenges in controlling the edge structures and stabilization of hole defects. Exploring the properties at the local structure of hole defects through in-situ experiments is also the important issue for the fabrication of realistic 2D nanopore devices.