3D carbon nanotube (CNT)-based macrostructures are the subject of extensive attention because the outstanding properties of 1D and 2D nanostructures have not been fully translated into key engineering applications. Generation of 3D CNT architectures with covalent junctions could endow the new materials with extraordinary mechanical properties. In this study, detailed experimental characterization and statistical comparison are carried out on 3D boron-doped multiwalled CNT (CBxMWNT) sponges with covalent junctions and undoped multiwalled CNT (undoped-MWNT) sponges without junctions. By investigating the plastic, elastic, viscoelastic, and dynamic viscoelastic properties of both sponges, as well as the dependency of these mechanical properties on material morphology, the CBxMWNT sponge is found to be a more predictable and stable material than the undoped-MWNT sponge. Statistical comparison proves that the excellent properties of the CBxMWNT are attributed to its "elbow-like" junctions inside the 3D networks, which prevent permanent buckling and bundling of the CNTs under extreme loading. Thus, by optimizing the covalent junctions in 3D CNT sponges, their functional behavior can be controlled and regulated. These findings may promote applications of 3D CNT sponges in various fields, including biomedical or high-precision devices in which lightweight, controllable, and reliable mechanical properties are always desirable.