Porous carbon nanomaterials are widely applied in the electromagnetic wave absorption (EMWA) field. Among them, an emerging flower-like carbon nanomaterial, termed carbon nanoflowers (CNFs), has attracted tremendous research attention due to their unique hierarchical flower-like structure. However, the design of flower-like carbon nanomaterials with different magnetic cores for EMWA has rarely been reported. Herein, a general template method is proposed to achieve a set of high-quality magnetic CNFs, namely Co@Void@CNFs, CoNi@CNFs, and Ni@CNFs. The prepared magnetic CNFs have highly accessible surface area and internal space, rich heteroatom content, multi-scale pore system, and uniform and highly dispersed magnetic nanoparticles, as a result, deliver superior EMWA performance. Specifically, when the thickness is 2.6mm, the Co@Void@CNFs exhibit a maximum refection loss (RLmax) of -56.6dB and an effective absorption bandwidth (EAB) from 8.0 to 12.1GHz covering the whole X band. The CoNi@CNFs have an RLmax of up to -57.6dB and a wide EAB of 5.6GHz at just 1.9mm. For the Ni@CNFs, possess an ultra-broad EAB of 6.1GHz, covering the entire Ku band at 2.0mm. Overall, the hierarchical magnetic carbon nanoflowers proposed here offer new insights toward realizing multifunctional integrated carbon nanomaterials for EMWA.