In recent years, research in the field of dye/salt separation has been significantly progressed. However, issues such as poor permeability and low dye/salt separation factor remain unsolved. In response, we have developed a molecular engineering strategy to construct a MXene-based membrane with record-breaking performance. Crystal Violet (CV) molecules were initially used as electrostatic media to precisely adjust the interlayer spacing and orientation of MXene, resulting in the formation of an ordered honeycomb-like structure featuring three-dimensional interconnected channels. This configuration greatly shortened the pathways compared to traditional mass transfer channels. Theoretical calculations indicate that the CV molecules primarily engaged in strong interactions with the oxygen-containing functional groups on the surfaces of MXene layers, effectively regulating the hydrophilicity and steric hindrance effect within the channels. By introducing ECP 600JD Carbon (EC) particles as an intermediate layer, the self-defects of the composite membrane in the ultra-thin state were significantly repaired. Additionally, ultra-short hydrophilic mass transfer channels were established. As a consequence, Large Layered MXene@CV Ultra-thin Membrane/EC (LMCU/C) was successfully prepared, exhibiting excellent dye/salt separation performance and high permeability. This membrane demonstrated a permeance of 540.8 LMH/bar for CR/NaCl mixed solution, achieved a dye/salt separation factor of approximately 47, and maintained operational stability for 10 h, outperforming the majority of existing membranes. This work can provide fresh insights into strategies for designing membrane structures through molecular engineering.