This study aims to systematically investigate the short-term and long-term effects of magnetic microparticles (MPs) and nanoparticles (NPs) on critical flux in membrane bioreactors (MBRs). Comparison among six MBRs was carried out with different activated sludge samples. Results showed that the short-term adsorption and flocculation contributed only minimally, however, the long-term magnetic induced bio-effect improved the critical flux by conditioning sludge properties. Additional molecular weight distribution of soluble microbial product (SMP) indicated that long-term magnetic induced bio-effect declined the content of macromolecules (> 500 kDa and 300-500 kDa), but promoted the content of small molecules (< 100 kDa), consequently reduced the free energy of SMP gelling foulants, and further promoted the higher critical flux. Moreover, the magnetic MPs presented the better performance than NPs. This study illustrated that sufficient pre-acclimatization of magnetic activated sludge is significantly necessary to improve the critical flux in MBRs.