The extensive application of ceramic membranes in wastewater treatment draws increasing attention due to their ultra-long service life. A cost-effective treatment for high-strength swine wastewater is an urgent and current need that is a worldwide challenge. A pilot-scale sequencing batch flat-sheet ceramic membrane bioreactor (ScMBR) coupled with a short-cut biological nitrogen removal (SBNR) process was developed to treat high-strength swine wastewater. The ScMBR achieved stable and excellent removal of COD (95.3%), NH4+-N (98.3%), and TN (92.7%), though temperature went down from 20 °C, to 15 °C, to 10 °C stepwise along three operational phases. The COD and NH4+-N concentrations in the effluent met with the discharge standards (GB18596-2001). Microbial community diversity was high, and the genera Pseudomonas and Comamonas were dominant in denitritation, and Nitrosomonas was dominant in nitritation. Ceramic membrane modules of this pilot-scale reactor were separated into six layers (A, B, C, D, E, F) from top to bottom. The total filtration resistance of both the top and bottom membrane modules was relatively low, and the resistance of the middle ones was high. These results indicate that the spatial distribution of the membrane fouling degree was different, related to different aeration scour intensities demonstrated by computational fluid dynamics (CFD). The results prove that the membrane fouling mechanism can be attributed to the cake layer formation of the middle modules and pore blocking of the top and bottom modules, which mainly consist of protein and carbohydrates. Therefore, different cleaning measures should be adopted for membrane modules in different positions. In this study, the efficient treatment of swine wastewater shows that the ScMBR system could be applied to high-strength wastewater. Furthermore, the spatial distribution characteristics of membrane fouling contribute to cleaning strategy formulation for further full-scale MBR applications.