Two-dimensional (2D) transition metal carbides (MXene) possess attractive conductivity and abundant surface functional groups, providing immense potential in the field of electromagnetic wave (EMW) absorption. However, high conductivity and spontaneous aggregation of MXene suffer from limited EMW response. Inspired by dielectric–magnetic synergy effect, the strategy of decorating MXene with magnetic elements is expected to solve this challenge. In this work, zigzag-like Mo₂TiC₂–MXene nanofibers (Mo-based MXene (Mo–MXene) NFs) with cross-linked networks are fabricated by hydrofluoric acid (HF) etching and potassium hydroxide (KOH) shearing processes. Subsequently, Co-metal–organic framework (MOF) and derived CoNi layered double hydroxide (LDH) ultrathin nanosheets are grown inside Mo–MXene NFs, and the N-doped carbon matrix anchored by CoNi alloy nanoparticles formed by pyrolysis is firmly embedded in the Mo–MXene NFs network. Benefiting from synergistic effect of highly dispersed small CoNi alloy nanoparticles, a three-dimensional (3D) conductive network assembled by zigzag-like Mo–MXene NFs, numerous N-doped hollow carbon vesicles, and abundant dual heterogeneous interface, the designed Mo–MXene/CoNi–NC heterostructure provides robust EMW absorption ability with a reflection loss (RL) value of −68.45 dB at the thickness (d) of 4.38 mm. The robust EMW absorption performance can be attributed to excellent dielectric loss, magnetic loss, impedance matching (Z), and multiple scattering and reflection triggered by the unique 3D network structure. This work puts up great potential in developing advanced MXene-based EMW absorption devices.