Membrane filtration is regarded as one of the promising technologies for water treatment. However, insufficient micropollutants removal and membrane fouling still limited the further application. Herein, this study engineered a novel membrane hybrid system integrating typical pharmaceuticals removal and membrane self-cleaning by assembled layered MXene and hexagonal boron nitride (h-BN). By doping a small amount of MXene into h-BN (mass ratio of 1 to 10), the synergetic process of adsorption and photocatalytic degradation were achieved. Based on experimental and density functional theory (DFT) calculation results, the chemisorption-photodegradation performance of the membrane hybrid system assembled with 1/10 MXene@h-BN was significantly enhanced due to the termination group and conductive property of MXene. In addition, trimethoprim (TMP) degradation by the above membrane followed the Langmuir–Hinshelwood model, indicating pollutants removal initiated not only on the membrane surface but also in the bulk solution under simulated solar irradiation. This phenomenon was attributed to the generation of •OH and 1O2 by forming Ohmic contact with altered internal band structure. The durability and practical experiments with secondary effluent from local wastewater treatment were also tested. The exceptional self-cleaning performance of the membrane hybrid system assembled with 1/10 MXene@h-BN was demonstrated by lower membrane fouling and maintaining durability even after five cycles. Furthermore, the performance (both pollutants removal and flux) of the modified membrane for secondary effluent treatment was also considerable, validating its potential for practical application. Owing to the excellent features, the membrane assembled with MXene@h-BN is anticipated to be an ideal candidate for advanced wastewater treatment.