As the utilization of nanolaminates composed of two-dimensional (2D) materials has become promising candidates for precise molecule/ion separations, precisely controlling the size, chemistry and configuration of the intra-nanochannel is crucial for further development of membranes. Herein, we developed covalently functionalized MoS2 membranes with amino acids (AAs) pillars via polarized N-Mo bonding for substantially improving the selectivity and permeability towards high-concentration salts and micropollutants. The optimized Glycine-Proline configuration in tailorable nanochannels, combined with the steric hindrance imposed by the protruding AAs and the ion-confined partitioning of Pyrrole-N and Carboxyl-O functionalities, contribute to achieving selectivity of MgCl2/Na2SO4 up to 11.2 and 8.1 in single and binary solutions. Meanwhile, the synergy between the hierarchical network of water pathways and the decorated hydrophobic pyrrolidine rings effectively facilitates low-friction water transport across the confined nanochannels. Impressively, the improved HM-GP demonstrates rejection rates of 95.7% for 0.6 M NaCl with a water flux of 15.2 l m−2 h−1 bar−1 under osmosis-driven condition, and it maintains a high salt rejection of 93.2% with a water flux of 17.5 l m−2 h−1 in pressure-driven process. This work not only offers an efficient strategy for designing robust HM-GPs with great potential in sustainable water purification and ion sieving, but also provide valuable guidance for developing separation technologies based on 2D material membranes.