Pure organic nature and nanoporous structure make covalent organic frameworks (COFs) a promisingly potential candidate in mixed matrix membranes (MMMs). However, COFs-based MMMs have hardly ever been applied in water purification due to their hydrolytic nature. In this study, we elaborately selected TpPa-2 with extensive stability in complicated water-environments as nanofiller to prepare MMMs for water treatment for the first time. Microwave synthetic technique was employed and optimized to construct the TpPa-2(MW) with a much higher BET surface area, smaller particle size, less agglomeration tendency and excellent stability. TpPa-2 was also synthesized mechanochemically (MC) for comparison to indicate how the synthetic technique influences the TpPa-2 and TpPa-2-incorporated MMM5. Membrane structure and property, water transport capacity and separation performance of both TpPa-2(MW)- and TpPa-2(MC)-incorporated MMMs were comprehensively investigated. It proved that our MMMs with an ultralow amount (0.2 wt%) of TpPa-2(MW) featured both improved water flux and rejection, breaking the trade-off between permeability and selectivity for polymer membrane. A membrane forming mechanism was further proposed to understand the effectiveness of TpPa-2(MW) in MMMs. This new generation COFs-based MMMs would be highly efficient, resource saving and cost-effective, which promise a great potential application in practical water purification.