This study aims to explore the feasibility of biochar as a carrier to improve the simultaneous removal of nitrogen and phosphorus in biological aerated filters (BAFs) for treating low C/N digested swine wastewater (DSW). Two similar BAFs (BAF-A with hydrophobic polypropylene resin as fillers and BAF-B with bamboo biochar as carrier) were developed for DSW treatment. Results showed that the NH-N, TN, and TP removal performances in BAF-B were higher than those in BAF-A. Carrier type had an obvious influence on the structures and diversity of the microbial population. The biochar carrier in BAF-B was conducive to the enrichment of the functional microorganisms and the increase of microbial diversity under high NH-N conditions. Microbial analysis showed that the genera Rhodanobacter (10.64%), JGI_0001001-h003 (14.24%), RBG-13-54-9 (8.87%), Chujaibacter (11.27%), and Ottowia were the predominant populations involved in nitrogen and phosphorus removal in the later stage of phase III in BAF-B. BAF with biochar as carrier was highly promising for TN and TP removal in low C/N and high NH-N DSW treatment.