Three-dimensional covalent organic frameworks (3D COFs) with spatially periodic networks demonstrate significant advantages over their 2D counterparts, including enhanced specific surface areas, interconnected channels, and more sufficiently exposed active sites. Nevertheless, research on these materials has met an impasse due to serious problems in crystallization and stability, which must be solved for practical applications. In this Minireview, we first summarize some strategies for preparing functional 3D COFs, including crystallization techniques and functionalization methods. Hereafter, applications of these functional materials are presented, covering adsorption, separation, catalysis, fluorescence, sensing, and batteries. Finally, the future challenges and perspectives for the development of 3D COFs are discussed.