Although different metal–organic framework (MOF) membranes have been widely studied for gas separation, their application for water treatment is still in its infancy. MOF membranes with improved hydrophilicity and stability are particularly essential for water/wastewater treatment. Herein, we have successfully developed heterogeneous membranes (Zn/Co-ZIF-L) composed of vertically standing leaf-like crystals of Zn-ZIF-L grown in situ onto porous ceramic supports, followed by the subsequent heterogeneous growth of Co-ZIF-L. The heterogeneous membranes show improved hydrophilicity (WCA = 13.6 ± 1.6°) and enhanced anti-bacterial adhesion. Significantly, they simultaneously deliver a relative high water flux and much improved anti-bacterial adhesion when compared with the homogeneous membranes (Co-ZIF-L and Zn-ZIF-L). The improvements are attributed to the intrinsic hydrophilic nature of Co-ZIF-L, their epitaxial growth onto Zn-ZIF-L as well as the increased surface roughness. The success of constructing a heterogeneous MOF structure shows an effective strategy to achieve the hydrophilic MOF membranes with considerably enhanced stability for water treatment.