Nitrite is normally removed slower than nitrate in sulfur-based autotrophic denitrification (SADN), and this may cause nitrite accumulation and decrease the efficiency of nitrogen removal. However, this study shows that nitrite was removed faster by SADN coupled with anaerobic ammonium oxidation (anammox). Both a coupled system and a control system were established to verify the preferential nitrite removal process and to explore the potential causes. The results showed that the removal efficiencies of nitrite and nitrate in SADN of the coupled system were 100% and 69.9%, respectively, under excess nitrite. In anammox effluent, the pH and ORP increased to 8.60 ± 0.11 and −286 ± 21.92 mV, respectively, jointly creating suitable reduction conditions for preferential nitrite removal. Furthermore, the protein-like substances present, C10-HSL and C14-HSL, were increased by 1130.875 a.u. to 5.35 and 1.13 ng L⁻¹, respectively. These changes promoted the activity of nitrite reductase and the abundance of Longilinea, Thiobacillus, and Methyloversatilis. The synergistic effect of material flow and information flow in the coupled system caused preferential nitrite removal. This study provides new insight towards solving the nitrite accumulation problem in the practical nitrogen removal process.