Covalent organic frameworks (COFs) have emerged as functional materials for various potential applications. However, the availability of three-dimensional (3D) COFs is still limited, and nearly all of them exhibit neutral porous skeletons. Here we report a general strategy to design porous positively charged 3D ionic COFs by incorporation of cationic monomers in the framework. The obtained 3D COFs are built of 3-fold interpenetrated diamond net and show impressive surface area and CO2 uptakes. The ion-exchange ability of 3D ionic COFs has been highlighted by reversible removal of nuclear waste model ions and excellent size-selective capture for anionic pollutants. This research thereby provides a new perspective to explore 3D COFs as a versatile type of ion-exchange materials.