Crack assessment of bridge piers using unmanned aerial vehicles (UAVs) eliminates unsafe factors of manual inspection and provides a potential way for the maintenance of transportation infrastructures. However, the implementation of UAV‐based crack assessment for real bridge piers is hindered by several key issues, including the following: (a) both perspective distortion and the geometry distortion by nonflat structural surfaces usually appear on crack images taken by the UAV system from the pier surface; however, these two kinds of distortions are difficult to correct at the same time; and (b) the crack image taken by a close‐range inspection flight UAV system is partially imaged, containing only a small part of the entire surface of the pier, and thereby hinders crack localization. In this paper, a new image‐based crack assessment methodology for bridge piers using UAV and three‐dimensional (3D) scene reconstruction is proposed. First, the data acquisition of UAV‐based crack assessment is discussed, and the UAV flight path and photography strategy for bridge pier assessment are proposed. Second, image‐based crack detection and 3D reconstruction are conducted to obtain crack width feature pair sequences and 3D surface models, respectively. Third, a new method of projecting cracks onto a meshed 3D surface triangular model is proposed, which can correct both the perspective distortion and geometry distortion by nonflat structural surfaces, and realize the crack localization. Field test investigations of crack assessment of a real bridge pier using a UAV are carried out for illustration, validation, and error analysis of the proposed methodology.