Nanosized zeolite molecular sieves are increasingly explored for developing high-performance nanocomposite membranes, mainly because of their ordered pore structures and remarkable thermal stability. In this study, hierarchical nanosized aluminophosphate molecular sieves AlPO-5 (AFI) were synthesized as functional fillers to construct thin-film nanocomposite (TFN) membranes. Nanosized AlPO-5 was effectively positioned onto porous polysulfone supports via a filtration-assisted method, followed by in situ interfacial polymerization to construct a polyamide layer atop the modified supports. The synthesized nanosized AlPO-5 crystals have both intrinsic micropores and abundant intracrystalline mesopores. SEM and AFM analyses reveal that the introduction of AlPO-5 not only enhanced the surface roughness of TFN membranes with valley-shaped surface but also substantially decreased the thickness of a polyamide layer compared to nodular-shaped TFC membranes. These differences are mainly ascribed to retarded piperazine diffusion and positioned AlPO-5 nanoaggregates. The role of AlPO-5 loading in overall separation performance of TFN membranes was studied. The best-performing TFN membranes showed the highest water permeability of 23.2 L m−2 h−1 bar−1, nearly twice that of unmodified TFC membranes, while maintaining a high salt rejection of 97.5%. The thickened and roughened polyamide layer with reduced transport resistance as well as intrinsic abundant mesopores of AlPO-5 fillers mainly contribute to the enhanced water transport. This study highlights the usage of hierarchical zeolite molecular sieves to fabricate high-permeable polyamide membranes for elevated nanofiltration performance. Nanosized AlPO-5 that features intrinsic micropores and abundant intracrystalline mesopores was utilized for fabricating thin-film nanocomposite membranes with rapid water transport for elevated nanofiltration performance. Display omitted •New TFN membranes were fabricated by introducing AlPO-5 fillers via IP reaction.•The presence of AlPO-5 increases the surface roughness and surface hydrophilicity.•AlPO-5 modified membranes have a higher MWCO and lower crosslinking degree.•TFN membranes have markedly increased water flux with comparable salt rejection.