The development of three-dimensional (3D) functionalized covalent-organic frameworks (COFs) is of critical importance for expanding their potential applications. However, the introduction of functional groups in 3D COFs remains largely unexplored. Herein, we report the first example of 3D Salphen-based COFs (3D-Salphen-COFs) and their metal-containing counterparts (3D-M-Salphen-COFs). These Salphen-based COFs exhibit high crystallinity and specific surface area in addition to excellent chemical stability. Furthermore, the Cu(II)-Salphen COF displays high activity in the removal of superoxide radicals. This study not only presents a new pathway to construct 3D functionalized COFs but also promotes their applications in biology and medicine.