Magnetic core-shell structural mesoporous carbon materials have an extensive application prospect in microwave absorption because of their comprehensive merits of magnetic function and distinctive mesoporous structure. Herein, magnetic core-shell structural carbon nanotubes@mesoporous N-doped carbon (CoNi/CNTs@mesoNC) nanofibers are successfully fabricated by combining homogeneous coating of mesoporous polydopamine, surface deposition of CoNi-bimetal metal-organic frameworks (MOFs), and in-situ growth of CNTs and CoNi nanoparticles. The resultant CoNi/CNTs@mesoNC nanofibers possess a well-defined hierarchical structure consisting of CNTs core and mesoporous carbon shell distributed with short CNTs and CoNi nanoparticles, high surface area (∼316 m2 g−1), high nitrogen content (∼5.5 wt%), and large pore size (∼10 nm). As expected, the rational design of multifunctional components and hierarchical structure endows CoNi/CNTs@mesoNC composites with excellent microwave absorption performance. Particularly, the minimum reflection loss can reach −52.1 dB at 13.4 GHz with only 1.7 mm thickness and the corresponding effective absorption bandwidth is up to 5.2 GHz (12.8–18.0 GHz), outperforming most reported microwave absorbing materials. The microwave absorption mechanism of this material has been deeply investigated and systematically clarified. This work provides meaningful reference for the design and fabrication of functional core-shell microwave absorbers with distinctive mesoporous structure.