•A CNT–necklace-liked hybrid 3D nanostructure has been first designed.•Carbon spheres could be in situ form with solderless joint on the CNTs.•An exceptional shielding effectiveness (exceeding 30 dB) value was achieved.•Shielding mechanism has been thoroughly investigated. Recently, a novel 3D nanostructured materials that consists of different types of carbon materials via covalent C–C bond has greatly enhance the performance due to synergistic combination of different carbon forms. In this work, carbon spheres are seamlessly grown on the 3D CNT hybrid architectures loading nickel that serves as template and a CNT–necklace-liked hybrid 3D nanostructure has been fabricated by using chemical vapor deposition for the first time. This type of carbon spheres possessed magnetic characteristic and a high density of carbon spheres were grown on its joint, which exceeds 30 dB in X-band. Shielding mechanism has been thoroughly investigated on the base of far field theory of electromagnetic shielding to demonstrate that the estimated shielding effectiveness values are consistent with experimental results.