Heteroatom nitrogen doping and morphology control have been considered as the effective approaches for improving electromagnetic wave (EMW) absorption ability of carbon-based absorbers. Herein, by controlling the adding dosage of pyridine, thickness controllable MOF-derived [email protected] carbon ([email protected]) hexagonal nanoflakes presented increased content of doped N atoms and tunable morphology from nanorods-, nanoparticles- to nanoflakes-like. Moreover, it made it possible to adjust the electromagnetic parameters of [email protected] The 3D conductive network of carbon framework and magnetic Ni nanoparticles could be obtained from the converted MOF precursor. The controllable dimension and morphology of N-doped carbon skeleton endowed more electronic transportation paths, better anti-reflection surfaces, higher conduction loss and polarization relaxation, while the evenly distributed Ni nanoparticles provided considerable multiple resonances and eddy current. All of these characteristics contributed the electromagnetic wave absorption (EMA) with improved dielectric loss, magnetic loss and impedance matching. The analysis indicated that the sample with 30 wt% of [email protected] showed the widest bandwidth, which was 6.21 GHz ranging from 11.79 to 18.00 GHz with a thickness of 2.3 mm, while the corresponding radar band was the whole Ku band (12.0–18.0 GHz). Our research provided a valuable approach for fabricating high-efficiency microwave absorption materials by combining the control of morphology and N-doped effect on the absorbers.