Black phosphorus quantum dots (BPQDs) show great promise as anode material for sodium-ion batteries (SIBs) due to their high theoretical capacity and short ion diffusion pathways. However, the challenges of low electronic conductivity and aggregation of BPQDs hinder their performance in SIBs. Loading BPQDs onto MXene nanosheets can address these issues, but the two-dimensional nanosheets may restack into a dense film during the filtration process, limiting reaction kinetics. Here, we report, for the first time, a bionic strategy for multilayer honeycomb-like MXene/BPQDs (MLHM/BPQDs) hierarchical architecture anode for SIBs. MXene nanosheets are arranged to ordered honeycomb layers and interlayer channels through the dual-template method. MXene nanosheets are arranged to ordered honeycomb layers and interlayer channels through the dual-templates method, and then, BPQDs are uniformly self-assembled onto the inwalls of the honeycomb. The unique open hierarchical architecture serves as an excellent substrate for rapid electron transport. Its large specific surface area offers more sites for BPQDs loading, preventing aggregation, and provides abundant channels and space for electrolyte infiltration and BPQDs volume change. The -O terminal groups increased after annealing, and the abundant -O/-F terminal groups on the surface of MXene can effectively enhance the binding energy and diffusion rate of Na+. The synergy of structure and surface chemistry accelerates the kinetics for MLHM/BPQDs, delivering a high reversible capacity of 653 mAh g−1 after 500 cycles at 2 A g−1 (94.3% capacity retention), which demonstrates its great potential as a SIBs anode material.