Porous carbon nanotubes/cobalt nanoparticles (CNTs/Co) composite with dodecahedron morphology was synthesized by in situ pyrolysis of the Co-based zeolitic imidazolate framework in a reducing atmosphere. The morphology and microstructure of the composite can be well tuned by controlling the pyrolysis conditions. At lower pyrolysis temperature, the CNTs/Co composite is composed of well-dispersed Co nanoparticles and short CNT clusters with low graphitic degree. The increase of pyrolysis temperature/time promotes the growth and graphitization of CNTs and leads to the aggregation of Co nanoparticles. The optimized CNTs/Co composite exhibits strong dielectric and magnetic losses as well as a good impedance matching property. Interestingly, the CNTs/Co composite displays extremely strong electromagnetic wave absorption with a maximum reflection loss of −60.4 dB. More importantly, the matching thickness of the absorber is as thin as 1.81 mm, and the filler loading of composite in the matrix is only 20 wt %. The highly efficient absorption is closely related to the well-designed structure and the synergistic effect between CNTs and Co nanoparticles. The excellent absorbing performance together with lightweight and ultrathin thickness endows the CNTs/Co composite with the potential for application in the electromagnetic wave absorbing field.