Two-dimensional (2D) material membranes have significant potential for selectively transporting molecules and ions, crucial for environmental and energy applications significantly. However, challenges such as complex pathways and instability due to weak interactions hinder their performance. This study takes 2D MXene (Ti3C2Tx) as a platform and proposes a lattice vacancy-anchored chemical etching method to perforate MXene nanosheets and produce acid cross-linkers simultaneously. The etching process involves H2O2 oxidation consuming Ti atoms from the lattice vacancies of MXene to create peroxo titanic acid (PTA), precisely generating nanopores in the nanosheets for additional transport pathways. At the same time, the produced PTA acts as a cross-linking agent that enhances the interaction between MXene nanosheets to form stabilized interlayer channels. This approach results in multilevel features in the MXene membrane, offering abundant vertical water channels and robust interlayer ion-sieving channels. Consequently, both permeability and selectivity improve nearly 10-fold compared to the pristine membrane, overcoming previous trade-offs. This strategy presents a precise and ingenious method for perforating 2D materials and constructing high-performance mass transport channels of 2D membranes at various levels, benefiting sustainable and highly efficient desalination processes.