2D transition metal carbides and carbonitrides (MXenes) have emerged as promising electrode materials for electrochemistry ion capture but always suffer from severe layer-restacking and irreversible oxidation that restrains their electrochemical performance. Here we design a dual strategy of microstructure tailoring and heterostructure construction to synthesize a unique 3D grape string-like heterostructure consisting of Ti3C2Tx MXene hollow microspheres wrapped by fungi-derived N-doping carbon nanoribbons (denoted as GMNC). The 3D grape string-like heterostructure effectively avoids the aggregation of Ti3C2Tx MXene sheets and enhances the stability of MXenes, providing abundant active sites for ion capture, and an interconnected conductive bionic nanofiber network for high-rate electron transport. In consequence, GMNC achieves a superior adsorption capacity for sodium ions (Na+) in capacitive deionization (CDI) (162.37 mg gNaCl-1) with an ultra-high instantaneous adsorption rate (30.52 mg g-1 min-1) at an applied voltage of 1.6 V and satisfactory cycle stability over 100 cycles, which is a strong performer among the state-of-the-art values for MXene-based CDI electrodes. In addition, in situ electrochemical quartz crystal microbalance with dissipation monitoring (EQCM-D) measurement combined with density functional theory (DFT) reveals the mechanisms of the Na+ capture process in the GMNC heterostructure. This work opens a new avenue for designing high-performance MXenes with a 3D hierarchical heterostructure for advanced electrochemical applications.