Direct discharge of livestock wastewater seriously harms the environment, due to the significant changes in water quality and quantity it brings forth, and the high concentrations of organic matter, ammonia nitrogen, and phosphorus the waste water contains. Here, changes in pollutant removal performance and microbial community structure of a kind of pre-acidified high-strength livestock wastewater were investigated on laboratory scale by means of the anaerobic-aerobic sequencing batch reactor (SBR) under different influent loading conditions. The results showed that the removal rates of the total nitrogen (TN), orthophosphorus (PO3-4—P) and chemical oxygen demand (COD) in the high load influent processed by the SBR reached 64.5%, 97.5% and 94.5%, respectively. The reactor presented shortcut nitrification with simultaneous accumulation of NH+4—N and NO2—N, which may be related to the effect of high influent loading on the activity and populations of ammonia-and nitrite-oxidizing bacteria. The enhanced biological phosphorus removal activity of the sludge was higher when propionate was used as the carbon source instead of acetate. The relative abundance of glycogen accumulating organisms (GAOs) increased significantly with the increase of influent loading. Tetrasphaera was the consistently dominant polyphosphate accumulating organisms (PAOs) in the reactor and contributed significantly to phosphorus removal performance. With a high concentration of organic matter, there was no significant substrate competition between PAOs and GAOs in SBR, and the nitrogen and phosphorus removal performance of the system was not affected.