The demand of nanofiltration (NF) membranes for practical and cost-effective environmental treatment is exploding. Mixed matrix membranes (MMMs) have attracted tremendous interest on account of combining the benefits of polymer and inorganic fillers. In this study, mesoporous silica thin films with perpendicular nanochannels (SBA-15(⊥)) incorporated in chitosan (CS) were fabricated for dye wastewater purification. Functional groups, such as amino or epoxy groups were introduced into SBA-15(⊥) (SBA-15(⊥)-NH 2 , SBA-15(⊥)-Epo) for forming covalent bonds with chitosan matrix to improve their compatibility. The excellent performance in dye/salt fractionation in aqueous solution was demonstrated by SBA-15(⊥)-Epo/CS MMMs, which realized a cut off of 585 g/mol, 99.9% rejection of Congo red, while maintaining 85% permeation of NaCl. In addition, the separation mechanism of the resulting membrane was explored. The efficient NF performance of SBA-15(⊥)-Epo/CS membrane was attributed to its better compatibility between SBA-15(⊥)-Epo and chitosan matrix by virtue of the formation of covalent bonds thus to ensure the high dye rejection, and the vertically oriented nanochannels arrangement facilitated the molecule transportation. This work will inspire feasible synthesis of a new generation of MMMs membranes for dye wastewater purification.