Abstract: The wave-absorbing materials are kinds of special electromagnetic functional materials and have been widely used in electromagnetic pollution control and military fields. In-situ integrated hierarchical structure construction is thought as a promising route to improve the microwave absorption performance of the materials. In the present work, layer-structured Co-metal-organic frameworks (Co-MOFs) precursors were grown in-situ on the surface of carbon fibers with the hydrothermal method. After annealed at 500°C under Ar atmosphere, a novel multiscale hierarchical composite (Co@C/CF) was obtained with the support of carbon fibers, keeping the flower-like structure. Scanning electron microscope, transmission electron microscope, X-ray diffraction, Raman, and X-ray photoelectron spectroscopy were performed to analyze the microstructure and composition of the hierarchical structure, and the microwave absorption performance of the Co@C/CF composites were investigated. The results showed that the growth of the flower-like structure on the surface of carbon fiber was closely related to the metal-to-ligand ratio. The optimized Co@C/CF flower-like composites achieved the best reflection loss of −55.7dB in the low frequency band of 6–8 GHz at the thickness of 2.8 mm, with the corresponding effective absorption bandwidth (EAB) of 2.1 GHz. The EAB of 3.24 GHz was achieved in the high frequency range of 12–16 GHz when the thickness was 1.5 mm. The excellent microwave absorption performance was ascribed to the introduction of magnetic components and the construction of the unique structure. The flower-like structure not only balanced the impedance of the fibers themselves, but also extended the propagation path of the microwave and then increased the multiple reflection losses. This work provides a convenient method for the design and development of wave-absorbing composites with in-situ integrated structure.