The development of wearable multifunctional electromagnetic protective fabrics with multifunctional, low cost, and high efficiency remains a challenge. Here, inspired by the unique flower branch shape of “Thunberg’s meadowsweet” in nature, a nanofibrous composite membrane with hierarchical structure was constructed. Integrating sophisticated 0D@2D@1D hierarchical structures with multiple heterointerfaces can fully unleash the multifunctional application potential of composite membrane. The targeted induction method was used to precisely regulate the formation site and morphology of the metal–organic framework precursor, and intelligently integrate multiple heterostructures to enhance dielectric polarization, which improves the impedance matching and loss mechanisms of the electromagnetic wave absorbing materials. Due to the synergistic enhancement of electrospinning-derived carbon nanofiber “stems”, MOF-derived carbon nanosheet “petals” and transition metal selenide nano-particle “stamens”, the CoxSey/NiSe@CNSs@CNFs (CNCC) composite membrane obtains a minimum reflection loss value (RLmin) of -68.40 dB at 2.6 mm and a maximum effective absorption bandwidth (EAB) of 8.88 GHz at a thin thickness of 2.0 mm with a filling amount of only 5 wt%. In addition, the multi-component and hierarchical heterostructure endow the fibrous membrane with excellent flexibility, water resistance, thermal management, and other multifunctional properties. This work provides unique perspectives for the precise design and rational application of multifunctional fabrics.