A simultaneous partial nitritation, anammox, denitrification, and COD oxidation (SNADCO) process was used to evaluate the nitrogen and biodegradable organic matter removal of swine manure digestate based on a nitrite limitation and ammonium surplus strategy. As influent ammonium concentration increased from 500 mg/L to 2100 mg/L, the 5 day biochemical oxygen demand (BOD5) maintained at a high removal efficiency of 95.4%. However, nitrogen removal efficiency (NRE) decreased from 90.9% to 68.2% due to the inhibition of AnAOB caused by an ammonium concentration of 2100 mg/L. The contribution of AnAOB to nitrogen removal was 75.6–86.5%, while that of denitrifying bacteria was 4.6–7.0%. In the case of COD removal, the contributions were from ordinary heterotrophic organisms and denitrifying bacteria, at 27.1–64.9% and 11.2–22.1%, respectively. The results of specific bacteria activity tests and microbial analysis showed that a highly efficient synergism between functional microorganisms is essential for the stability of the SNADCO process.