A novel polyzwitterionic hydrogel coated mixed matrix membrane (MMM) was successfully prepared, characterized and used for Cu2+, Mn2+, and Pb2+ heavy metal ions removal from water. Hydrophilic and porous covalent organic framework (COF) nanoparticles (NP) as filler were synthesized from melamine and terephthalaldehyde, and then incorporated into polyamide (PA) thin film composite (TFC) membrane. The hydrogel coating was applied by using a tailored cross‐linkable polymer system in combination with concentration polarization enabled cross‐linking. The effects of COF NP loading into PA layer and polyzwitterionic hydrogel coating on the membrane morphology and separation performance were studied using different analyses. The MMM prepared with a COF NP loading of 0.02 wt/wt% in the hexane dispersion used for NP deposition during PA layer formation (leading to 0.42 g/m2) exhibited an increased pure water permeability of around 200% compared with the neat PA TFC membrane while the Mn2+ ion rejection maintained above 98%. Scanning electron microscopy surface images and zeta potential profiles showed that the hydrogel was successfully deposited on the membrane surface. Furthermore, the hydrogel coating could decrease net surface charge of membranes but did not significantly influence the heavy metal ions rejections under nanofiltration conditions. The results of filtration experiment with protein solution indicated that the hydrogel coated membranes exhibited superior antifouling property, as shown by higher flux recovery ratio after washing with water, compared with neat PA TFC membrane and not coated MMM, respectively.