To address the severe membrane fouling caused by swine manure digestate, this study provides a systematic evaluation of how pore size governs purification efficiency and flux recovery. SEM-EDS and ATR-FTIR were employed to characterize the foulants across five different pore sizes. The results revealed significant differences in flux retention and permeate quality, with smaller-pore membranes exhibiting superior antifouling performance. At a volume reduction factor of 5, the flux decline rates of the 50, 200, 500, 800, and 1200 nm membranes were 34.7%, 8.8%, 33.6%, 40.5%, and 72.2%, respectively. Notably, the 200 nm membrane achieved the highest flux maintenance and recovery after chemical cleaning, whereas the 1200 nm membrane suffered the greatest flux decline and poorest effluent quality. The 800 nm membrane experienced severe fouling likely driven by particulate deposition and cake layer formation. Based on the combined characterization results, polysaccharides and protein-like substances are suggested to be the primary organic foulants. The proposed fouling mechanisms likely involve cake layer formation on the membrane surface, along with concentration polarization and pore blocking. Furthermore, the internal adsorption of soluble organics likely contributes to irreversible fouling. Overall, this study not only elucidates the pore size-dependent fouling mechanisms but also establishes the 200 nm ceramic membrane as a highly promising pre-treatment candidate for digestate concentration processes.