To achieve the in situ capacity expansion of the post-denitrification biological aerated filter (BAF-DN), the integration of BAF with the anammox process (BAF/AX) was proposed. With the objective of maximizing retaining ammonia nitrogen, the operational optimization of BAF was achieved by two distinct strategies. The treatment performance of BAF demonstrated that the removal efficiencies of chemical oxygen demand (COD) and ammonia nitrogen (NH4+-N) was 66.3~67.3% and 4~12%, respectively, under conditions of low aeration intensity (0.4 m3·m−2·h−1) or a shortened empty bed residence time (EBRT) of 30 min. Residual NH4+-N in the BAF effluent served as the ammonia substrate for the subsequent anammox process, which was successfully launched by using ceramic particles and sponges as carriers. Notably, the sponge carrier facilitated a shorter start-up period of 41 to 44 days. Furthermore, the sponge-based anammox reactor exhibited a superior NH4+-N removal capacity (≥85.7%), under operations of a shorter EBRT of 40 min, low influent NH4+-N concentrations (≤30 mg/L), and COD levels of ≤67 mg/L. In addition, a comprehensive evaluation of the BAF/AX process was conducted, which considered performance, cost-effectiveness, and engineering feasibility. The performance results illustrated that the effluent quality met the standard well (with a COD level of ≤ 50 mg/L, and a TN of ≤3.1~10.5 mg/L). Following a comparison against the low aeration intensity operation, it was recommended to operate BAF at a low EBRT within the BAF/AX process. Consequently, the treated volume was double the volume of the standalone BAF-DN, synchronously achieving low costs (0.413 yuan/m3).