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 2.6 mm, the Co@Void@CNFs exhibit a maximum refection loss (RLmax) of −56.6 dB and an effective absorption bandwidth (EAB) from 8.0 to 12.1 GHz covering the whole X band. The CoNi@CNFs have an RLmax of up to −57.6 dB and a wide EAB of 5.6 GHz at just 1.9 mm. For the Ni@CNFs, possess an ultra‐broad EAB of 6.1 GHz, covering the entire Ku band at 2.0 mm. Overall, the hierarchical magnetic carbon nanoflowers proposed here offer new insights toward realizing multifunctional integrated carbon nanomaterials for EMWA.