In addition to pore structure and surface charge, the charge spatial distribution within NF membranes plays a crucial role in ion transport process. However, precisely tuning this charge distribution remains a significant challenge. Here, we construct the mix-charged thin-film nanocomposite (m-TFN) membranes with tailorable charge spatial distribution for highly efficient Li+/Mg2+ separation by incorporating quaternary ammonium-functionalized UiO-66-QA nanocrystals into the interfacial polymerization process. The UiO-66-QA nanocrystals are synthesized via a facile post-synthetic modification. The addition of UiO-66-QA nanocrystals benefits to narrow pore size distribution and lower inner negative charge of the mix-charged polyamide nanofilms. Furthermore, these nanocrystals serve as both templates for ordered nanostructure formation and additional transport pathways, significantly enhancing water permeance. As a result, the m-TFN membranes, characterized by a heterogeneous charge distribution and uniform pore structure, exhibit remarkable Li+/Mg2+ selectivity of 323.93, along with competitive salt/water flux ranging from 227.22 ± 13.3 to 250.2 ± 7.4 L m−2 h−1, striking a better trade-off between Li+/Mg2+ selectivity and permeability. Moreover, the SDEM model analysis further reveals that it evidences a higher Li purity and Li recovery compared to current state-of-the-art NF membranes. This work presents a promising strategy for fine-tuning charge distribution and pore structure to achieve high-performance ion separation.